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add

[ Add column | Add matrix | Add slide | Add table ]

A family of commands adding things. Some commands use append syntax instead It is also used as an option equivalent to append in write command.

add one or several columns or header elements to an existing table

[ Add column function ]

Adding a single column/header

add column T I|R|S|P|i|r|s [name= s ] [index= i_pos] [mute]

add header T I|R|S|P|i|r|s|M|etc [name= s ] [mute]

(to add a row see add table args )

Adding multiple column/headers

add column T I|R|S|P|i|r|s I|R|S|P|i|r|s .. [name= S] [index= i_pos ] [mute]

add header T I|R|S|P|i|r|s|M|etc I|R|S|P|i|r|s|M|etc .. [name= S] [index= i_pos ] [mute]

this command adds one or several columns to an existing table in the i_pos column (in other words if you want you column to be in the 2nd position, specify 2 as an argument). The columns are append to the end of the table by default. If the table does not exist the command will create a new table.

It an integer, string, or real are specified as an argument instead of a column-array, this value is multipled to create a column of the appropriate size.

The mute option suppresses the info (equivalent to temporarily setting l_info=no ).

Examples:

add column t {1 2 3} # create a new table
add header t "A new table" name="title" # add a string to the header section
add column t {"a","b","c"} name="AA" # column AA is appended
add column t {"x","y","z"} index = 2 
# adding a chemical array
add column t Parray({"CC","CC(O)=O","CCO"} smiles) name = "mol" index = 1

# adding multiple arrays
add column t {1 2 3} {3 2 1} {"a","b","c"} Parray({"CC","CC(O)=O","CCO"} smiles) name={"A","B","C","mol"}
t
 #>T t
 #>-A-----------B-----------C-----------mol--------
    1           3           a          "CC"
    2           2           b          "CC(O)=O"
    3           1           c          "CCO"

See also: move column

Add dependent columns

add column T function=s_expression [name=s] [index= i_pos]

Adds a column defined by the s_expression, which may contain operations with other columns in the same table. The generating expression information is attached to the column, which allows to recalculate the values in the column using the same expression. The following functions are supported: "Ceil", "DrugLikeness" "Floor", "IupacName" "Log", "Max", "Mean", "Min", "MoldHf" "MolFormula" "MolLogP" "MolLogS" "MolPSA" "MolSymmetry" "MolVolume" "MolWeight" "Nof_Atoms" "Nof_Chirals" "Nof_HBA" "Nof_HBD" "Nof_Molecules", "Nof_RotB" "NofSites", "Normalize", "Real", "Rmsd", "Sign", "String", "Sum".

Examples:

add column T Chemical( {"c1(c(nc(N)nc1O)O)N", "c1c[nH]c2C(N=C(N)Nc12)=O"} ) name="mol"
add column T function="MolWeight(mol)" name="MW"
add T # add new row
T.mol[3] = Chemical("CC")
build column T.MW # recalculate mol. weights, setting the value for the new row

add column T2 {1 2 3} {4 5 6}
add column T2 function = "A+B"  # sum of two columns

See also: build column

Adding real arrays as matrix rows

add matrix [ M ] R

adds a matching row R to matrix M . If the matrix does not exist it is created with the default name (the name is saved in s_out ) Example:

add matrix M {1. 2.} # creates new matrix M
add matrix M {3. 3.} # adds a row
show M
 #>M M
 1. 2. 
 3. 3.

add slide to a slideshow.

add slide [i_posInCurrentSlideshow] [s_slideTitle] [comment = s_slideComment] [ display= "-option|-option" ]

adds a slide to the slideshow table. This table contains one parray, called slideshow.slides . If the slide position is not specified the slide will be added to the end. Alternatively, it will be inserted after the specified i_posInCurrentSlideshow

Normally the slide is saved with window layout, and graphical parameters. Those can be ignored if you add the display="-.." option. The options can be used either in the on mode, e.g. "-layout", or in the off mode, e.g. "+layout" (all on by default) :

• "-layout" # ignores the window/panel layout
• "-smooth" # ignores smooth view transitions between slides
• "-add" # do not overwrite the previous slide views, just add to it
• "-gf" # ignore graphical representations, inherit them
• "-color" # ignore colors , inherit them
• "-labeloffs" # do not display labels
• "-viewpoint" # ignore viewpoint changes
• "-graphopt" #
• "-mol" # do not display the chem-table window
• "-grob" # do not display grobs
• "-map" # do not display maps
• "-all" # switches off all the above properties

Example:

build string "ala ala ala"
display ribbon a_ 
display xstick a_/12,13 magenta
add slide "My View" comment = "These two residues are particularly dear to me" display="-layout"
undisplay # hide all
# wait..
display slide "My View" # bring it back

See also: display slide , Slide

Add / insert table rows. Append tables.

add T_1 [ i_RowNumber ] [ T_2 | row_selection ]
add/insert rows (or another table with the same coloumns) to table T_1 at the target row position i_RowNumber . Use 1 (one) if you need to insert the first line. If the second table or selection is not provided, the command adds an empty row. The row_selection can contain rows from the same table or from a different table with a matching column structure. In the latter case, the columns may be matched by their names regardless of column order. Default values are inserted for all absent columns. The defaults for an empty line are empty string or zero value for strings or numbers, respectively. The target position will then correspond to the index of the first inserted row.

From version 3.6-1e the add tableName command also returns the current row as i_out .

Examples:

 
group table t {1 2 3} "a" {"b","d","e"} "b" 
show t 
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    3           e 
 
add t 1 # insert empty line before 1st  
show t 
 #>T t 
 #>-a-----------b---------- 
    0           ""  
    1           b 
    2           d 
    3           e 
 
group table t {1 2 3} "a" {"b","d","e"} "b" # recreate the table 
add t 3 t[1]  # insert a duplicate of 1st row after the 2nd  
show t
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    1           b 
    3           e 
 
group table t {1 2 3}  "a"  {"b","d","e"} "b"  # recreate the table 
group table tt {1 2 3} "c" {"b","d","e"} "b" {4 5 6} "a" # another table 
# order is diffferent, extra column present  
add t 3 tt[1:2]  # or add t 3 tt.aa<3  
show t 
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    4           b 
    5           d 
    3           e 

 
 alias seq sequence                    # seq will invoke sequence  
 alias delete seq                      # delete alias name seq  
 alias dsb display a_//ca,c,n          # abbreviate several words to  
                                       # reduce typing efforts  
                                       # aliases with arguments  
 alias NORM ($1-Mean($1))/Rmsd($1) 
 show NORM {6,7,8,4,6,5,6,7,5,6}       # make sure there is no space 

[ Align res numbers | Align sequence | Align fragments | Align 3D | Align 3D heavy ]

Examples:

 
 read pdb "1crn" 
 align number a_1            # renumber all res. 1 to N 
 align number a_1/10:20 101  # just the selected residues from 101 
 align number a_1       101  # renumber all res. 101 to 100+N 
 read pdb "2ins"
 align number a_/* 1
 align number a_/* 1 molecule # each chain starts from 1

 
 seqmaster = Sequence("ACDEFGHIKLMNPQRST") 
 build string   "--DEFGH-----PQRST"  # dashes are skipped    
 make sequence a_1 name="seqmodel"   # sequence is auto-linked 
 a = Align(seqmodel,seqmaster)       # linked alignment 
 align number a_1 seqmaster 
 # Info> residues of a_def.m renumbered by sequence 'seqmaster' from alignment 'a'    
 display residue label  

align sequence [selection] | seq1 seq2 .. | seedSequence [ min_seqID (20.)] [ name=s ]
make a multiple alignment of specified sequences. The sequence group may result from the group sequence s_groupName command. The input arguments include the following:

• seq1 seq2 ... : explicitly specified
• sequence : all sequences in the shell
• sequence selection : all sequences selected in GUI
• seqGroup : sequences grouped together previously
• seedSequence : sequences in the shell similar to the specified with optional min_seqID (default 20%).

For pairwise alignment use the Align( seq1 seq2 ) function. The algorithm includes the following steps (inspired by corridor discussions with Des Higgins, Toby Gibson and Julie Thompson ):

1. align all sequence pairs with the ICM ZEGA algorithm, and calculate pairwise distances between each pair of aligned sequence with the Dayhoff formula, e.g. the distance between two identical sequences will be 0. , while the distance between two 30% different sequences will be around 0.5. The distance goes to an arbitrary number of 10. for completely unrelated sequences. The distance matrix D_ij can later be extracted from the alignment with the Distance( ali_ ) function.
2. build an evolutionary tree from D_ij with the "neighbor-joining algorithm" of Saitou, N., Nei, M. (1987) to determine the order of the alignment and calculate relative weights of sequences and profiles from the branch lengths. The tree will be saved in the file defined by the tree= s or filename= s option . Starting from version 3.5-2 the aligTree.eps file is NO LONGER saved by default). The so-called Newick tree description string will be saved in s_out .
3. traverse the tree from top to bottom, aligning the closest sequences, sequence and profile or two profiles. After each Needleman and Wunsch alignment, build the profile.
4. generate the final neighbor-joining evolutionary tree and write the PostScript file with the tree to disk.

 
   read sequences s_icmhome+"zincFing"  
   list sequences               # see them, then ...  
   group sequence alZnFing      # group them, then ...  
   align alZnFing               # align them
   align alZnFing filename="znTree.eps"  # eps file with a tree

 
  read sequence swiss web "12S1_ARATH"
  read sequence swiss web "12S2_ARATH"
  group sequence arath
  align arath

[ sim4 ]

The procedure has the following steps: sequences are sorted by length the longest sequence is chosen as the seed sequence unless it is explicitly provided the longest sequence from the remaining set is aligned to the seed sequence using the external sim4 program. the output of this program is parsed and translated into the icm alignment the consensus sequence is created and becomes the master sequence the procedure is repeated until all the sequences are processed the multiple sequence alignment is further cleaned to compress spurious gaps when possible. This cleaning makes the consensus much more compact. The result of this command is best displayed with the show color ali_ command.

 
 read sequence "http://www.ncbi.nlm.nih.gov/UniGene/" + \ 
     "download.cgi?ID=5198&ORG=HsLINE=1" # 
 read sequence "../Hs5198" 
 group sequence unique u # squeeze out obvious redundancies and form group 'u' 
 align new u             # form multiple alignment and build consensus 
 show color u 

• filtering, group sequence unique=".."
• Trans ()
• show [color] ali_

This command finds the residue alignment (or residue-to-residue correspondence) for two arbitrary molecules having superposable parts of the backbone conformations. The structural alignment identification and optimal superposition is primarily based on the C-alpha-atom coordinates, but the sequence information can be added with a certain weight (the default value of r_seqWeight is 0.5 which was found optimal on a benchmark). The structural alignment algorithm is based on the ZEGA (zero-end-gap-alignment) dynamic programming procedure in which substitution scores for each i,j-pair of residues contain two terms:

• structural similarity in a i_windowSize window between two fragments surrounding residues i and j, respectively. This similarity is calculated as local Rmsd of the residue label atoms (these atoms are C-alpha atoms by default but can be reset to other atoms with the set label command, e.g. set label a_*.//cb ). If the option distance is specified the deviation of the interatomic distances between equivalent pairs of atoms (so called distance rmsd ) is calculated instead of a more traditional root-mean square deviation between atom coordinates of equivalent atoms. The latter method is less accurate but an order of magnitude faster.
• sequence similarity (if r_seqWeight > 0.). Average local sequence alignment score in the i_windowSize window is calculated for i,j-centered pair of fragments. In this sense this sequence similarity is different from the one used in pure sequence alignment (see the Align function), in which just the i,j residue pair is evaluated. The default value of r_seqWeight of 0.5 is rather mild (about a half of the structural signal).

• ali_out contains structural alignment (if sequences linked to the molecules do not exist, they will be created on the fly). The alignment can be further edited with the interactive alignment alignment editor.
• as_out contains the residue selection of the aligned residues in the first molecule
• as2_out contains the residue selection of the aligned residues in the second molecule
• M_out , the matrix of local structural/sequence similarity in a window is retained and can be visualized by:

Example:

 
read pdb "1ql6"
read pdb "2phk"
align a_1ql6. a_2phk.
make grob color 10.*M_out name="g_mat # x,y,z scales 
display g_mat 
# or 
plot area M_out display grid link 

• Align( seq_1 seq_2 distance|superimpose ). This function creates the first unrefined structural alignment as described above.
• find alignment which refines initial structural alignment.

 
  a = Align(... superimpose )  # superposition/RMSD based local str. alignment 
  a = Align(... distance    )  # distance RMSD based local str. alignment 
 
  find a superimpose 4.0 0.5 

 
  read pdb "1brl" 
  read pdb "1nfp" 
  rm a_*.!A 
  display a_*.//ca,c,n 
  color molecule a_*. 
  align a_2.1 a_1.1 
  center 
  show String(as_out) String(as2_out) 
  color red as_out 
  color blue as2_out 
  show ali_out 

• r_rmsd = 1. A
• i_windowSize = 15 residues
• i_minFragment = i_windowSize
• r_elongationWeight=0.1

 
 read pdb "4fxc" 
 read pdb "1ubq" 
 display a_*.//ca,c,n 
 color molecule a_*. 
 align heavy a_1.1 a_2.1 12 1.5 .1 
 center 
 load solution 2            # load the second best solution 
 color red  as_out 
 color blue as2_out 
 for i=1,10 
   load solution i 
   color molecule a_*. 
   color red  as_out 
   color blue as2_out 
   pause                     # rotate and hit 'return' 
 
 endfor 

[ Append sequence | Append stack | Append column ]

Appending sequences to a sequence group or an alignment

append ali_seqGroup seq_1 seq_2 .. .
appends sequences to a sequence group. This may be required if you formed a sequence group for future alignment or filtering/compression and you want to append additional sequences to it.

Examples:

 
read sequence group "bunch.seq" name="xx" # group xx is formed 
append xx my_seq  # appending your sequence to xx 
group xx unique   # filter out identical ones 
align xx 

read sequence swiss web "12S1_ARATH" 
read sequence swiss web "12S2_ARATH"
group sequence name="arath"
read sequence swiss web "14310_ARATH"
append arath 14310_ARATH
align arath

Appending a molecule or a ligand stack to an existing stack

append stack s_ligandStackFileName [i_maxConf]

append stack os_ligandObject

this command takes a stack which corresponds to a receptor object and appends each conformation in the stack with a conformation of the ligand. If the ligand conformation can be taken from either from a stack file, this command will combine each conf from the main stack with all conformations from the file. The i_maxConf argument will set the limit on how many conformations are taken from the ligand stack (i.e. append stack "lig.cnf" 1 will combine only the first conformation of the ligand )

If the second argument is an ICM object, each conf of the current stack will be extended with the variables from the ligand. Now the ligand object can be appended to the receptor object with the move command and the new combined object can use the expanded stack.

build string "ACDEF"  # the "ligand" peptide
rename a_ "Lig"
translate a_ {10. 0. 0.} # shift not to overlap with a_Rec.
montecarlo v_//!?vt*     # created Lig.cnf stack

build string "RSTVW"  # the "receptor" peptide
rename a_ "Rec"
montecarlo v_//!?vt*     # created Rec.cnf stack

move a_1. a_2.    # ligand must be the 1st argument
append stack "Lig.cnf" 4 # combine up to 4 best ligand confs
minimize stack    # minimizes each stack conf
load conf 1       # check them out

append two tables via two columns with matching values

append t1.A t2.B
Append rows of table t2 to table t1 by rows corresponding to unique column t2.B . The t1.A column values do not need to be unique.

 
group table people {"J","C","M"} "p" {"MS","MS","MS"} "orgid" 
group table orgs  {"MS"} "id" {"Molsoft"} "name" 
append people.orgid orgs.id 
people 
 #>T people 
 #>-p-----------orgid-------name------- 
    J           MS          Molsoft 
    C           MS          Molsoft 
    M           MS          Molsoft 

This command is a particular case of a more general join command.

See also the add table command for adding rows from a column with identical column structure (e.g. add t tt ).

assign

[ Assigns structure | assign sstructure segment ]

 
 read pdb "1crn" 
 assign sstructure a_/* "_"  # make everything look like a coil 
 cool a_ 
 assign sstructure a_/1:10 "HHHH_EEEEE"   
 cool a_ 

This command does not change the geometry of the model, it only formally assigns secondary structure symbols to residues. Note: to change the conformation of the selected residue fragment, according to a desired secondary string, use the ICM -object and the set command applied to both sequences and molecular objects.

 
 nice "1est"       # notice that many loops look like beta-strands 
 assign sstructure # now the problem is fixed 
 cool a_ 

assign sstructure segment [ ms_molecules ] # ms_ICMmoleculesPreferable
create simplified description of protein topology (referred to as segment representation). Segments shorter than segMinLength are ignored. The current object is the default. This command will work both on un converted pdb files as well as the pdb files. However the resulting secondary structure will be BETTER when the structure is converted and hydrogens are added.
See also show segment, ribbonStyle, display ribbon. convert convertObject

 
   for i = 1, 8 
     print "Now i = ", i, "and it goes up" 
     if (i == 4) then 
       print "... but at i=4 it breaks, Ouch!" 
       break 
     endif 
  endfor 

[ Build atom | Build column | Build sequence | Build model | Build loop | Build smiles | Build string | Build hydrogen | Build molcart ]

• from sequence file ( build s_seqfile )
• from sequence string ( build string)
• from a linear chemical notation ( build smiles )
• from a sequence and a template by homology ( build model )

build atom as1 [simple] [s_elementName=("c")] [i_bondType=(1)]
by default it will add a carbon to the selected atom in a non-ICM object and rebuild hydrogens for the affected atoms. Use the strip command for ICM objects.

Options and arguments:

• simple does not rebuild hydrogens.
• s_elementName is a string with the name of the chemical element.
• i_bondType is 1 for a single bond (the default), 2 for a double bond and 4 for a triple bond.

Example:

build smiles "CC(C)Cc1ccc(cc1)C(C)C([O-])=O" name="ibuprofen"
strip a_ibuprofen.
build atom a_ibuprofen.m//c1 "n"
build atom a_ibuprofen.m//c1 2

See also:

• make bond
• delete bond
• delete atom

Recalculating dependent columns

build column T.col

Rebuilds all values in a dependent column T.col

build column T_ | T_row_selection

Rebuilds all dependent columns in the table T_ or row selection (e.g. T[12], or T.ID==123 ) If column A depends on column B and column B depends on other columns, column B will be calculated before column A.

Examples:

add column T {2 5 1} name="B"
add column T function="A + B" name="C"
add column T function="C + B" index=1 name="D"
T.A[1] = 10
build column T[1] # should change values of C and D in the first row

See also: add column function

Building object from sequence file

build s_IcmSeqFileName [ library= { s_libFile | S_libFiles} ] [ delete ]
reads s_IcmSeqFileName.se ICM-sequence file and builds an ICM molecular object. This sequence file is different from a simple sequence file and contains three (sometimes four) character residue names defined in the icm.res residue library file (try show residue types to see the list).

Use command build string if you want to build an object from a string with one letter coded sequences or a named sequence. E.g. build string "ASDGF" or "ASD;DERR" or "nh2 ala his cooh"

To get a D-amino acid instead of L-ones simply use D as a prefix: Dala Darg. Specify N- or C-terminal modifiers directly in the file if needed. The build command will create them in some default conformation (extended backbone with different molecules oriented around the origin as a bunch of flowers). Several molecules can be specified in the ICM sequence file.
Residue names may contain numbers (i.e. 4me ). However, the residue numbers with a modification character, such as 44a, 44b should contain a slash before the modification character (i.e. 44/a , 44/b ). An example in which we create a sequence of residues ala and 4me with numbers 2a and 2b, respectively: "se 2a ala 2b 4me".
The library option lets to temporarily switch the library file. The same result may also be achieved by redefining the LIBRARY.res array of the LIBRARY table.
The delete option temporarily sets the l_confirm flag to no and the old object with the same name gets overwritten. Examples:

 
 build "def"  # def.se file
 build s_icmhome + "alpha.se"  # alpha.se file  
 build "wierd" library="mod.res"  # get residues from mod.res  
# 
 LIBRARY.res = {"icm","./myres"} 
 build "s"  

[ Homology steps | Loop search | The output ]

Possible modes:
• simple one-to-one mode: build model seq_1 [ms_1] [ali_1]
• N sequences - N corresponding molecules: build model seq_1 seq_2 .. seq_N ms_1,2,..N This mode requires the minimize tether command to complete the construction.

 
 l_autoLink = yes 
 read pdb "x"  
 read alignment "sx"  
 build model ly6 a_  
 ribbonColorStyle = "alignment" # grey-gaps, magenta-insertions 
 display ribbon 

 read pdb "2ins"  # multichain  
 a = Sequence( "GIVEQCCASV CSLYQLENYC N" )
 b = Sequence( "VNQHLCGSHL VEALYLVCGE RGFFYTPKA" )
 c = a
 d = b
 build model  a b c d a_1. 
 minimize v_//V "tz" 1000
# or   minimize tether
# Now optimize the side chains 
 selectMinGrad = 1.5 
 set vrestraint a_/* 
 montecarlo fast v_/!I/x*   
# !It means residues which are not Identical to their template residues 
# use  refineModel to energetically optimize the model 

 
align number a_/* 

 
set vrestraint a_/*  # assigns the rotamer probabilities 
montecarlo fast v_/Cx/x* # x* selects for all chi (xi) angles 

 
set vrestraint a_/*  # assigns the rotamer probabilities 
montecarlo v_/14/x*   
ssearch v_/14/x*     # systematic conformational search for the 14-th sidechain 

The output

The build model command returns the following variables:
LoopTable master table containing list of all the loops, their conformation in alphanumeric code, a measure of the deviation of the database loop ends and the model attachment sites, the loop length and the numerical conformation type (not really important). E.g.

 
#>T LoopTable 
#>-1_Loop------2_Conf------3_Rmsd------4_Nof-------5_Type----- 
   a_ly6.a/7:10 31R21       0.1         11          1           
   a_ly6.a/60:63 1RRR32      0.1         8           1           
   a_ly6.a/43:46 211331RRRR  0.240658    4           1           

 
icm/ly6> LOOP1 
#>T LOOP1 
#>-Conf--------energy------offset------rmsd------- 
   31R21       0.          3623594     0.092104    
   31RR2       1.519275    3427772     0.083372    
   R1121       1.612712    3750108     0.097777    
   R1R32       1.639177    1529882     0.087113    
   R1RR2       1.880638    3806768     0.079335    
   31R32       3.714823    4561270     0.053853    
   R3RR2       4.531406    4003324     0.042881    

 
 read object s_icmhome+"crn" 
 build loop a_/20:26  # rebuild this loop 

build smiles s_smiles_string [ name= s_ObjName]

create an ICM-object from the smiles -string, respectively. Set l_readMolArom to no if you do not want to assign aromatic rings from a pattern of single and double bonds (and formal charge and bond symmetrization for CO2, SO2, NO2or3, PO3 ) upon building. To suppress suppress the symmetrization and consequential charging of CO2, set the l_neutralAcids flag to yes .

Examples:

 
build smiles "CCO"   # ethanol 
 
build smiles "Oc(cc1cc2)ccc1cc2N" 
 
build smiles "Oc(cc1cc2)cc(ccc3)c1c3c2" 

build smiles "C/C=C\C" # cis-2-butene

build smiles "C/C=C/C" # trans-2-butene
 
              # dicoronene 
build smiles "c1c2ccc3ccc4c5c6c(ccc7c6c(c2c35)c2c1c1c3c5c6c"+\ 
             "(c1)ccc1c6c6c(cc1)ccc1ccc(c5c61)cc3c2c7)cc4" 
 
              # NAD 
build smiles "[O-]P(=O)(OCC1OC(C(O)C1O)N1C=2N=CN=C(N)C=2N=C1)"+\ 
             "OP(=O)([O-])OCC1OC(C(O)C1O)N=1C=CC=C(C=1)C(=O)N" 
 
              # Hexabenzo(bc,ef,hi,kl,no,qr)coronene 
build smiles "c1c2c3c4c(ccc3)c3c5c(c6c7c(ccc6)c6c8c(ccc6)c6c9"+\ 
             "c(ccc6)c(cc1)c2c1c9c8c7c5c41)ccc3"  
 
              # rubrene 
build smiles "c1c2c(c3ccccc3)c3c(c(c4ccccc4)c4c(cccc4)c3c3ccccc3)"+\ 
             "c(c2ccc1)c1ccccc1" name="rubrene"

Sometimes the build smiles command is not sufficient. The molecule needs to be optimized in the mmff force field and several conformations need to be sampled. A more rigorous conversion is provided by the convert2Dto3D macro.
See also: Smiles , find molecule.

Building object from string

build string s_IcmSequence [ name= s_ObjName ] [ delete ]
create an ICM-object from a s_IcmSequence string (see the build command above). To get a D-amino acid instead of L-ones simply use D as a prefix: Dala Darg. Specify N- or C-terminal modifiers directly in the file if needed. The build command will create them in some default conformation.

The build string command also understands short one line version of the full format. The short format looks like "ASD" or "ala his" and can not start from "ml " or "se ".

The possibilities are the following:

• one letter code, - it needs to be specified in upper case letters, e.g. "DD";
• full three-four letter code, e.gg. "nter ala hise Dala cooh"
• multiple molecules - just use a comma, a semicolon or a dot as a separator, e.g. "WWWW;AAAA;EEE" or "ala his trp; nh3+ gly coo-"

 
   build string "ADGHRTE" # the charged terminal groups will be added
   build string "ADGH;RTE" # two peptides, a and b 
   build string "nter ala Dhis cooh" name="pep"  # one peptide named a_pep. 
   build string "ml a \nse nh3+ his coo- \nml b \nse trp" # molecules a and b  
   build string IcmSequence("GHFDSFSDRT","nter","cooh") # translate and add termini 
# 
# Using alias  BS   build string "se $0" 
   BS ala his trp   

Building hydrogens according to topology and formal charges.

build hydrogen [ as_heavyAtoms ] [ i_forcedNofHydrogens ] [cartesian]
adds hydrogens to the specified heavy atoms according to their type and formal charge. All heavy atoms of the current object are used by default. If your have hydrogens already and their configuration is wrong, you can delete them with the delete hydrogen command. The number of hydrogens may be enforced if the optional i_forcedNofHydrogens argument is specified.

Option cartesian means that no new hydrogens are added, but, rather, the existing ones are set to new coordinates according to the heavy atoms (a better syntax for this action is set hydrogen ).

See also the set bond type command, set hydrogen .
Examples:

 
  read mol s_icmhome+ "ex_mol"  # several small molecules  
  display a_4. 
  build hydrogen a_4.  # added and displayed  
#  
  undisplay
  display a_3.
  build hydrogen a_3.
# move one of the nydrogens  
  build hydrogen a_3. cartesian # should put the hydrogen back at a correct position

Building molcart indices for substructure, similarity or exact search

build molcart {s_tableName|S_tableNames} [sstructure|similarity|exact]

builds (or rebuilds) various keys for molcart table.

call

call s_ScriptFileName [ only ]
invokes and executes an ICM-script file. End the script with the quit command, unless you want to continue to work interactively, or use it in other script.
The option only allows to suppress opening the script file if the call command is inside a block which is not executed. By default the script file is opened and loaded into the ICM history stack anyway, but the commands from the file are not executed.
The absolute path of the script can be obtained by calling the Path ( last ) function.
Example:

 
  call _startup             # execute commands from _startup file  
  show Path( last )

if Type( CONSENSUS ) != "table" then
 call _startup only # only means do not read if the table is already loaded
endif

• only : do not rescale, translate only, i.e. move the selected atoms to the center of the graphics window
• static : scale only according to the visible X-Y dimensions and the margin. Do not take the Z-dimension into account in the size calculation as if you do not intend to rotate objects. That implies an assumption that the orientation of molecules/grobs/maps will not be changed.

 
   nice "1est" 
   center                        
   center Sphere ( a_/15:18 )    
   center a_/1:2 only  # keep the scale 
 
   read grob s_icmhome+"beethoven" # a genius  
   display beethoven smooth 
   center beethoven static   # 10 A margin 

[ clear-error ]

clear terminal screen
clear selection clear the graphical selection as_graph

Example:

nice "1crn"
as_graph = a_/1:5 # select five residues
clear selection # nothing again

clear pattern chemarray

clear SMARTS search attributes in the input chemical array.

Example:

add column t Chemical("[C;D2]")
clear pattern t.mol   # D2 attribute will be cleared

See also: Exist pattern

clear graphic [ os_ ] clears display properties , graphic representation memory and reset the graphic planes to the default.

clear error

clears all error and warning bits previously set by ICM. See also Error ( i_code )

[ Color specification | Color object ]

• : color all|{wire|xstick|cpk|surface|skin|[residue|atom|variable|string] label|ribbon [base]} [full]
• : color {molecule|object|alignment | R_values [window=] } [full] [all]
• : color background|volume # volume for the depthcuing fog color
• : color chemical { | pharmacophore }
• : color site index=
• : color distance|hbond|angle|torsion
• : color accessibility ([0:1]) # occlusion coloring
• : color [add|pseudo] GROB.atomColorRadius=
• : color map []
• : color |grob potential [ fast ] [ reverse | simple ] [] # electrostatic coloring
• : color [ ] [ ] [ auto ]

Options:

• full : allows to set colors for atoms that are not displayed in addition to the displayed ones. The default only changes colors of the atoms visible in a given representation. (this option has been added in versions compiled after Sep 15, 2009). This option replaces the set color command for batch coloring.
• all : colors all graphical representations (by default it colors only the specified ones)

See also set color to set atom or residue color directly and without graphics.

Specifying colors in ICM

There are various ways to specify a color in ICM: by name, index or RGB representation.

color_name | color[i_index] | i_Color | r_Color | rgb=rgb_color

Specifying color by name:

color red

Requesting contrasting colors by index:

color color[4]

Example:

  read pdb "1crn"
  display ribbon a_1crn.
  show colors 
  color a_/1:5/* color[89] 
  for i=1,Nof(a_/*) 
    color a_/$i color[i]       # speckled coloring 
  endfor 

color 3

Color indices are taken from the "rainbow" section of the icm.clr file. Currently there are 128 colors (i=0,127) in this section and they form a smooth transition from blue to red via white (not really a rainbow). You may change the "rainbow" colors in the icm.clr file. Number 128 becomes blue again. Using integer color indices is convenient for automatic coloring within ICM loops.

Example:

 
   display "Colors" 
   for i=1,255 
     color background i 
     print i 
   endfor 

Specifying colors interpolated between indexed colors:

color 4.5 

The color 4.5 will be the average between the "rainbow color" 4 and "rainbow color" 5.
Specifying colors by their RGB representation

Color is defined as a combination of red, green and blue components. The triple may be specified in different formats:

rgb = R_3rgb

- as an array of 3 reals in 0..1 range

rgb = I_3rgb

- as an array of 3 integers in 0..255 range

rgb = s_#rrggbb

- as a string where each component is defined by two characters in hexadecimal form. Optionally prefixed with a hash symbol ("#").

Examples setting magenta color (mixture of red and blue):

color rgb={255,0,255}
color rgb={1.,0.,1.}
color rgb="#ff00ff"
color rgb="ff00ff"

In case the requested RGB color is not available for the graphics system, ICM finds the closest color.

Coloring molecular objects

The main color command:
color [ as_ ] graphic_representation [ color_spec ]

color [ as_ ] graphic_representation [ I_colors | R_colors ] [window = R_2MinMax]

graphic_representation, when specified, must be one of the following

wire | hbond | cpk | ball | stick | xstick | surface | skin | site | ribbon [base]

This command colors selected atoms ( as_ ) or graphics object(s) according to the specified color. It is possible to either specify a single color color_spec, or provide an array ( rarray or iarray ) of colors to color each element of the selection according to a certain property, as electric charge or Bfactor.

The scale is determined by the minimal and the maximal elements of the array, independently of the array length. First the numbers in the array are scaled so that its minimum corresponds to the first color in the "rainbow" section and its maximum to the last color. Then the scaled numbers are applied sequentially to the elements of the selection. If the number of elements in the array is shorter than the number of elements in the selection, the array is applied periodically. If the color array is longer than the selection, the excessive numbers are not used for coloring but (attention!) they will be used for scaling.

The window={ minValue, maxValue } option allows to provide a range for color mapping. It will be used instead of the array minimum-maximum value range as the range from which the color array elements will be mapped into the rainbow colors. Moreover, values in the color array will be clamped to be in the window range.

In the following example the Bfactor(a_/ simple) values which may range from large negative values to large values will be clamped to the [4.,40.] range.

  nice "1ekg"
  color ribbon a_/ Bfactor(a_/ simple) window=4.//40.

 
  read object s_icmhome+"crn"
  display a_crn.
  color a_//* Charge(a_//*) window={-1.,1.}

It is also possible to show a color bar in the graphics window by changing the GRAPHICS.rainbowBarStyle property.

Each of the command arguments has a default:

• objects as_: the current object ( a_ ) only. Hint: to color all objects, use a_* .
• graphic_representation: all except ribbon. Ribbons should be colored explicitly using a color ribbon command.
• color_spec. The default coloring is by atom type, except for the ribbon representation which is colored by secondary structure by default.

In DNA and RNA ribbons, bases can be colored separately (e.g. color ribbon base a_1/* white ), the default coloring being A-red, C-cyan, G-blue, T or U-gold.

Examples of how the defaults work:

 
 nice "1crn" 
 display       # also displays wire 
 color         # all except ribbon colored by atom type 
 color ribbon  # only ribbon of a_ by secondary structure type  
 color ribbon red         # only ribbon as specified 
 color a_/1:10 ribbon yellow # parts

More examples:

 
 build string "ASDWER"     # hexapeptide 
 display
 color a_/1:4 green    # the first four residues in green  
 color                 # return to default colors by atom type  

 
 read pdb "1crn"
 display a_1crn. only 
                       # color atoms according to their B-factor  
 color a_1crn.//* Bfactor(a_1crn.//*) 
                       # crambin's ribbon  
                       # from blue N-term to red C-term gradually  
 display a_/* ribbon only 
 color a_/* Rarray(Count(1 Nof(a_/* ))) ribbon 
 
                       # another crambin's ribbon  
                       # from blue N-term to red C-term gradually  
                       # thick worm representation 
 assign sstructure a_/* "_"  
 GRAPHICS.wormRadius= 0.9 
 display a_/* ribbon only 
 color a_/* Count(1 Nof(a_/* )) ribbon 

Coloring 2D molecules in a chemical table

color chemical X_chemarray P_model

calculates atom contributions to the total value calculated by the P_model if this model is

• linear. (PLS)
• built using counted fingerprints (no external column-descriptors)

color chemical X_chemarray pharmacophore

color by built-in pharmacophoric definitions The list of definitions can be listed like this:

icm/def> show pharmacophore type
name         codesmarts                        color
-------------------------------------------------------
Negative     [Qn]C(~[O;D1])~[O;D1]             #87cefa
Negative     [Qn]P(~[O;D1])(~[O;D1])(~[O;D1])~*#87cefa
Negative     [Qn]S(~[O;D1])(~[O;D1])(~*)~*     #87cefa
Positive     [Qp][N;D3;$(N(-[*;^3])(-[*;^3])-[*;^3])]#fa8072
Positive     [Qp][N;D2;$(N(-[*;^3])-[*;^3])]   #fa8072
Positive     [Qp][N;D1;$(N-[*;^3])]            #fa8072
Positive     [Qp]C(~[N;D1])~[N;D1]             #fa8072
HBA          [Qa][O,S&v2,N&^2&X2,N&^1&X1,N&^3&X3]#98fb98
HBD          [Qd][!C;!H0]                      #ee82ee
Aromatic     [Qm]a                             #ffa500
Hydrophobic   [Qh][C&!$(C=O)&!$(C#N),S&^3,#17,#15,#35,#53]#e0ffff

How to color grob surface by depth

[ Color molecule | color background | color by alignment | color grob | color label | color map | color volume ]

color accessibility g_mesh [ r_maxShade ]

modify the color of each surface element of a grob to create perception of depth. The procedure calculates for each surface element (triangle) the extent it is occluded from ambient light by other parts of the molecule, and makes the elements darker proportionally to occlusion. Thus, concave regions such as pockets become dark since the surrounding bulk of the protein blocks the light from most directions, while protrusions remain bright since they are well exposed. Repeated application of the command or using a larger r_maxShade (the default is 0.8) generates a more dramatic shading of the shape.

Example:

color accessibility g_electro 0.7
color accessibility g_electro 0.7 # applying it two times may help to create a more dramatic effect

  clrs = Color(g_electro)
  # change grob color, e.g. with color accessibility
  color grob clrs

Uniquely coloring by object, molecule, residue or atom

color graphic_representation [ as_molecules ] [object|molecule|residue|atom]
a special command to color the displayed and selected molecules differently. The graphic representation field can be either empty, or one of those: wire xstick cpk surface skin ribbon, residue label, atom label, site label, variable label . E.g. select graphically some atoms and do this:

color xstick as_graph & a_*.//c* molecule  
color ribbon as_graph object
color cpk as_graph molecule
color residue label as_graph residue

sets the background to the specified color color_spec in one of the supported formats .

Examples:

color background blue 

color background lightyellow

color background rgb={255,255,255} # white. integers in 0..255 range

color background rgb={0.,1.,0.} # green. reals in 0.. range

See also: rgb, color background example .

• residue type
• consensus character at the residue position in the alignment
• colors as provided by the CONSENSUSCOLOR table.

 
  read sequence s_icmhome+"sh3" 
  nice "1fyn" 
  make sequence a_1  # extract 1st sequence 
  group sequence sh3 
  align sh3 
   
  color a_1 ribbon alignment 
  display skin white a_1 molecule
  color a_1 alignment   # colors all representations including skin 

color grob

[ Color grob unique | Color grob matrix | Color grob by atom selection | Color grob map | Color grob potential ]

Color is a powerful mechanism of showing extra information on ICM grobs ICM grobs may have individual colors assigned to each vertex, which allows to use grob coloring to illustrate properties of 3D surfaces.

The simplest way to set grob color is to paint it to a single color.

color g_grobName color_spec

colors the whole g_grobName grob to the color_spec color.

color grob color_spec

colors all grobs to color_spec.

Check out the color specification section for available color_spec options.

Example:

torus = Grob("TORUS",3.,1.)
display torus
color torus black # paint it black
color background white # this should improve the visibility
color torus rgb={127,255,212} # aquamarine, as some people call it

Automatic assignment of different colors to different grobs

color grob unique
In addition to the main color command which colors grobs there is a special command to automatically assign the displayed grobs to different colors.

See example for the split grob command.

Coloring grob by matrix of RGB values for each vertex.

color g_grob M_rgbMatrix
allows to set individual colors to grob vertexes. Colors are specified in RGB format in the M_rgbMatrix.Each row of the matrix is an RGB triple. This type of matrix may be obtained by the Color( g_grob ) function.

Examples:

torus = Grob("TORUS",3.5,0.5)
display torus smooth
n = Nof(torus)
R_rgb = Count(1 n/2)/Real(n/2) // Count(n-n/2 1)/Real(n-n/2)
add matrix M_rgb R_rgb
add matrix M_rgb Rarray(n,0.3)
add matrix M_rgb Rarray(n,0.7)
color torus Transpose(M_rgb)

This command allows to create special effects, like gradual disappearance of a grob into background:

# set the scene
color background black

# uncomment these lines to get a more sophisticated example
# torus = Grob("TORUS",3.5,0.5)
# display torus smooth 
# color torus blue

# the active grob
g = Grob("SPHERE",3.,5)  # a wire sphere  
display g smooth 
color g Random(Nof(g),3, 0., 1.) # color randomly 
M_colors = Color(g)               # extract current colors 
# make the sphere disappear (modern poetry)  
for i=1,20    # shineStyle = "color" makes it disappear completely 
 color g (1.-i/20.)*M_colors  
endfor         
for i=20,1,-1 # bring the sphere back  
 color g (1.-i/20.)*M_colors  
endfor 

color g_grobName as_closeAtoms color_spec [add|pseudo]

colors vertices of the grob which are less than GROB.atomSphereRadius to any of the selected atoms. The default value for the radius is 4Å.

Options:

• add : adds van der Waals radius for each atom to the GROB.atomSphereRadius parameter
• pseudo : for hydrogen bonding acceptors considers distances from LONE-PAIR centers at 1.7A distance from the acceptor atoms. If an atom is not an acceptor, the atom itself is considered. Note that a_//HA is a selection for hydrogen bonding acceptors and a_//HD is the donor selection.

Example in which we color 1.3 radius sphere around the lone pairs of hydrogen bonding acceptors:

color a_REC.//HA g_pocket magenta pseudo  GROB.atomSphereRadius=1.3

See color specification for the definition of color_spec.
See also: Grob( g R_6) function to return a patch of certain color.

Example:

nice "1crn"
make grob skin a_1crn. name="g_1crn"
display g_1crn
color g_1crn green
color g_1crn a_1crn.//1:60 red # color a patch by atom proximity

See also: make grob skin, make grob potential .

Coloring surfaces by 3D scalar field

color g_grob map map_Name I_transferFunction R_2mapValueBounds [ color_spec ]
colors vertices of the g_grob by the values of the map_Name . The map values at each grid point are first clamped into the R_2mapValueBounds range, then this range is divided according to the number of elements in the transfer function and each point is colored according to the value of the transfer function. The optional color_spec parameter is explained in the color specification section.
The new color will be mixed with the current color of grob points. Therefore if you want to color each of 3 RGB channels with a different normalized property value, first color the grob black, and then color with the red , green , or blue color depending on which channel you intend to use. Note that zero in the transfer function correspond to no color . Corresponding grob nodes will not be colored.
Transfer function is the same to the one in color map but has certain differences. This function (e.g. {0 0 0 1 2 3} ) contains any number of positive integers. 0 means "do not color", and each positive value is a scaling factor for the color provided as an argument, or a parameter to select a color from a predefined rainbow. In the above example, the R_2mapValueBounds range will be divided into 6 ranges and each value range will be colored accordingly.
Example in which we color the vertices of a grob by inverted values of truncated hydrophobic potential:

 
  read obj s_icmhome+"data/xpdb/1sre.ob"
  display a_	
  make grob skin a_2 a_2 name="g_pocket"        # create g_pocket 
  make map potential "gs" Sphere( g_pocket a_1) 
  compress g_pocket 1. 
  color g_pocket black 
  color g_pocket map -m_gs { 0,0,0,3,4,5 } { 0. 0.5  } green           
  display g_pocket
  h = Transpose( Color( g_pocket ) )[2]  # extract hydrophobicity 

Coloring grob by electrostatic potential

color g|grob potential [ fast ] [ reverse | simple ] [ms_sourceAtoms]

(REBEL feature) calculates electrostatic potential waterRadius away from the surface of the g_skin graphics object and color surface elements according to this potential from red to blue. Important the location of the center of the water probe is determined by the grob normal ( you can change it with the set g_ reverse command). If you compute the potential at a blob outside the molecule but with the normals point outwards, use the reverse option. To compute potential without any positional correction including normals use the simple option. The potential is calculated either by the REBEL boundary element solution of the Poisson equation, or, if option fast is specified, by a simple Coulomb formula with the dielConstExtern dielectric constant (78.5 by default).

The local value of potential is clamped to the range [ -maxColorPotential, +maxColorPotential ]. It means that a potential larger than maxColorPotential is represented by the same blue color, while values smaller than maxColorPotential are represented by the same red color. The real range is reported by the command and you can adjust maxColorPotential to cover the whole range. To suppress the absolute maxColorPotential threshold and use auto-scaling instead set maxColorPotential to 0. The color bar with values will appear according to the GRAPHICS.rainbowBarStyle preference. There are two macros to generate potential-colored skins: rebel and rebelAllAtom
The second one (given below) considers all the atoms (including hydrogens) with their charges.
The mean value of the potential at the surface is returned in r_out , and the root mean square deviation of the potential is return in r_2out shell variables, respectively. The averaging is free from bias due to uneven density of grob points. It uses equal size cubes distributed evenly over the surface. The number of representative cubes used for the calculation is return in i_out .

Examples:

 
read object s_icmhome + "crn"
display a_1
make grob skin a_1 name="g_crn"
make boundary a_1
display g_crn
color g_crn potential

color label as_ [ I_colors | R_colors ]
Colors labels associated with the selected residues or atoms. A simple option is to specify a single color using color specification formats. It is also possible to provide colors for each atom using an iarray I_colors or rarray R_colorsIf no atom selection is specified, all labels are colored.
Examples:

 
 read object s_icmhome + "crn" 
 display a_//n,ca,c white 
 display label residue 
 color label a_/* Count(1 Nof(a_/*)) 
 #
 color label a_/5:10 magenta 

 read object s_icmhome + "crn" 
 display a_//n,ca,c white 
 display label residue 
 color label lightyellow 

color map_Name [ I_colorTransferFunction ] [ R2_fromTo ] [ auto ]
color the current or the specified map according to the color transfer function supplied as I_colorTransferFunction.
The default: By default the maps are colored in such a way that points with zero map values become transparent while values above and below zero are colored by shades of blue or red, respectively.
The R2_fromTo array of two elements allows to set the lower and the upper boundaries for the red and blue colors, respectively. All values above and below will be trimmed to the range. For electrostatic maps the array is set to -5.,5. by default.
In the auto mode all grid points are divided to Nof( I_colorTransferFunction ) color classes according to the normalized function value (sigma units around the mean value) and each class is colored as specified in the I_colorTransferFunction (0 means transparent).
If the number of I_colorTransferFunction elements is odd (2* n+1 ) the class boundaries are the following:

• -infinity
• Mean- n *sigma,
• Mean-( n -1)*sigma,
• Mean-( n -2)*sigma,
• ...
• Mean- 1*sigma,
• Mean
• Mean+ 1*sigma,
• ...
• Mean+( n -1)*sigma,
• Mean+( n )*sigma.
• +infinity

• {0 0 0 0 0,0 0 0 3 10} default map coloring, color only high densities (blue from 3 to 4 Sigma, red >4 Sigma). Comma only shows you where the mean is.
• {0 1 0} color only Mean+- 0.5*sigma nodes, ignore high and low densities.
• {1 0 2} color low and high densities by different colors, ignore densities around the mean.
• {1 2 3 0 5 6 7} similar the previous one, but with more grades

read pdb "1crn"
make map potential name="mpot"
color mpot {1 2 0 4 5}
# OR
color mpot

color volume color_spec

determines the color of the fog in the depth-cueing mode ( activated with Ctrl-D ). Format of color_spec is explained here.

For example, if you want that distant parts of you structure are darker (black fog), but the background is sky-blue, you will do the following:

 
color background lightblue   
color volume black  

[ Compare atom | Compare variables | Compare surface ]

sets a metric for calculating a distance between different conformations in a stack .
The goal of the two following compare commands is to provide a desired setting before the montecarlo command and stack operations. This command defines a filter which is used to decide how many and what conformations from the stochastic optimization trajectory are kept as low energy representatives of a certain area in conformational space. This metric is also used for the subsequent stack manipulations, e.g. compress stack.
The compare command defines the distance measure between molecular conformations which is used to form a set of different low energy conformers in the course of the stochastic global optimization procedure. The defined distance is compared with the vicinity parameter and determines whether two conformations should be considered different or similar (i.e. belonging to the same slot in the conformational stack). The compare command determines the spectrum of conformations that will be retained in the stack, accumulated during a montecarlo procedure. The default comparison set is a set of all free torsion variables (see compare vs_ ). Other methods compare atom RMSD with and without superposition, using chemical superposition, and compare only the atoms in the interface with a molecule ( compare surface ).

Please note that the compare command can change the compareMethod preference. Example:

  montecarlo v_//2 compareMethod ="chemical static"  # suitable for docking

See also montecarlo, compareMethod.

Compare by deviations of cartesian coordinates with or without superposition

compare [ static ] as_
The command needs to be run when Cartesian root-mean-square deviation for positions of selected atoms ( as_ ) as a distance measure between stack conformations. Set the vicinity parameter to about 2.0 Angstrom if you want to consider conformations deviating by more than 2 A as different conformational families.
By default the selected atoms in different conformations will be optimally superimposed before the coordinate RMSD is calculated. The static option suppresses superposition and measures absolute deviation of the coordinates between conformations. The static option is relevant for ligand atoms in docking simulations to a static receptor.
The result of this procedure is that an internal flag is set to perform cartesian RMSD calculations during montecarlo run, and a set of selected atoms is marked for comparison.

 
   compare v_//phi,psi            # compare ONLY the backbone angles  
   vicinity=30.0                  # consider two conformations  
                                  # with phi-psi RMSD < 30. as similar  
 
   compare a_2//ca static         # compare Cartesian deviations  
                                  # of the second molecule's alpha-carbon atoms  
                                  # without prior optimal superposition  
   vicinity=3.0                   # consider two conformations with second  
                                  # molecule deviation < 3 A as similar  

compare surface as_currentObjSelection | as_staticReferenceObject.
Similarly to compare static as_ it will look at absolute deviations of coordinates, but the comparison will be applied dynamically only to a patch sub-selection of the atoms in the current object in the selectSphereRadius (default 5. A) proximity to the non-current-object atoms of the as_ selection. The selection typically would look like this: a_activeIcmObject.//ca | a_staticPdbReceptorObject.//ca
Example:

 
 compare a_runObj.//ca | a_recName.//ca surface 

 
 read pdb "1bgs"     # a complex 
 read pdb "1a19.a/"  # the protein ligand only 
 convert  
...     # make maps and other actions to prepare protein-protein docking 
 compare a_//c* | a_1.1 surface  # will use only  
 selectSphereRadius = 7. 
... 
 montecarlo  

[ Compress grob | Compress stack | Compress binary ]

compress g_grobName1 g_grobName2 .. [ r_minimalEdgeLength=.5 ]

compress grob [ selection ] [ r_minimalEdgeLength=.5 ]
simplify a grob (graphical object) by eliminating/merging small triangles into bigger ones. This procedure allows to generate very "low-resolution" molecular surfaces. The default value of the r_minimalEdgeLength is 0.5 Angstroms. Typically compression with the 1. A minimal edge parameter reduces the number of triangles by an order of magnitude. The compression algorithm does not change the connectivity of the surface. Therefore you can still split the compressed grob and find the fully enclosed cavities.
The compress command returns the new number of verteces in i_out and the new number of triangles in r_out variables, respectively (for the last compressed grob only).
Example:

 
read pdb "1crn" 
make grob skin smooth name="g_1crn" # creates a grob with many triangles 
display g_1crn 
compress g_1crn 1. # significantly reduces the number of triangles in the grob
display g_1crn 
compress g_1crn 4. # further simplification of the grob
display g_1crn 

compress stack [ fast ] [ i_fromConfNumber i_toConfNumber ] [r_enerDiff]

Remove similar and/or high energy conformations from the conformational stack. During a montecarlo run, some conformations of the generated conformational stack may be substituted by newly calculated ones with lower energies. New conformations may violate the initially correct distribution of the conformations in the slots of the stack as defined by the vicinity parameter and by comparison mode specified by the compare command. The compress command compares all the pairs of the stack conformations, identifies pairs of conformations in which two conformations are separated by a distance less than the vicinity threshold, and removes the higher energy stack conformation from each close pair. Optional arguments i_fromConfNumber and i_toConfNumber define a subset of the conformations in the stack which are to be analyzed and compressed (if any). The whole stack (from the first to the last conformations) is processed by default.
Note that if two close conformations are compressed into the better energy one, the number of visits of the resulting conformation will be a sum of the two numbers of visits.
The fast option applies an iterative compression algorithm which can be several orders of magnitude faster but the result may slightly differ form the default compress. The fast algorithm algorithm performs the following steps:

1. sort conformations by energy
2. start from the lowest energy conformation
3. find all conformations with higher energy than the current conformation within vicinity .
4. delete similar conformations with higher energies and compress stack
5. move to the next conformation in the new sorted stack, make it current and go back to step 3

 
 build string "VTLFVALY" 
 mncallsMC = 5000 
 montecarlo   # generates stack
 write stack "f1" 
 delete stack # clean up and 
 montecarlo   # generates another stack 
 read stack append "f1"  #  
 compare v_/2:5/phi,psi  # compare settings are different 
 vicinity = 40.          #  
 compress stack fast 
 vicinity = 20.          # new vicinity 
 compress stack  
 compress stack  2.0  # remove confs > 2 kcal/mole higher than the lowest one

compress binary s_inputfile [ filename=s_gzipfile | delete ]

Compresses the s_inputfile file using GZIP algorithm. If the filename is specified, the compressed file will be saved as s_gzipfile.If the delete option is specifeid, the compressed file replaces the input file (in place compression). Otherwise (by default) .gz extension is added to produce the compressed file name.

Example:

read pdb "1crn"; make map potential name="x"; write map x # create x.map file

compress binary "x.map" delete # compress in place

connect

[ Connect molcart ]

connect none

connects selected molecules to the mouse for independent rotation (by the LeftMouseButton) and translation (MiddleMouseButton) with respect to the original coordinate frame.

Option append will add selected molecule to the previously connected molecules
Note, that rotations/translations in the connect mode actually change the atomic coordinates of the selected molecules and keep the coordinate system unchanged in your graphics window.
To restore the usual global mode (i.e. all objects/molecules are disconnected and the mouse does not change their absolute positions, but rather the point of view), hit the Esc key when the cursor is in the graphics window. To restore the global mode temporarily press the Shift button.
Use: connect none to switch back to the global connection Examples:

read pdb "1eff"
copy a_1eff. # create something else in the scene
display ribbon a_*.
connect a_1eff.
# move it around now
connect none # disconnect

connect molcart {S_host_user_pass_db|s_host s_user s_pass s_db} [name=s_connectionID]

Connects to the database server specified by the command parameters. It is possible to also specify the s_connectionID which will be assigned to the connection. Parameters returned by the Name(sql connect) may be used in this command.

connect molcart on

Reconnects to the current Molcart.

connect molcart refresh

Reconnects to Molcart using settings stored in user's preferences.

connect molcart filename=s_file [s_db] [name=s_connectionID]

Opens a Molsoft database file. Database name s_db and the s_connectionID may be specified.

connect molcart s_connectionID off

Disconnects specified Molcart connection. See molcart connection options for explanation

connect molcart local off

Closes all open database files.

See also: molcart, molcart connection options, list molcart, set molcart, Name molcart.

continue

continue

skip commands until the nearest endfor or endwhile .
Example:

 
for i=1,5 
  if i==3 continue  # do not print 3 
  print i 
endfor 

[ Convert comp | Convert fragments | Convert mol | Convert and reroot ]

The default convert command is best used to convert PDB entries which have explicit residue descriptions and usually do not have hydrogen coordinates. In this mode each residue name is searched in the icm.res file and the coordinates of the present heavy atoms are used to calculate the internal geometrical variables (bond lengths, bond angles, phase and torsion angles) for the full atom model.
The exact option: converting protein with unusual amino-acids
Some pdb-entries may contain non-amino acid residues, or modified amino-acid residues which do not need to be replaced by standard full atom library entries with the same name . In this case use the exact option. This option suppresses interpretation by short residue name and converts the existing atoms and bonds in single-residue molecules (amino acids in peptides and proteins will still be extended by hydrogens upon conversion, to suppress that conversion write the molecule as mol and read it back, then convert exact ). Option exact may be necessary because chemical compounds with a four-letter short name identical to one of the amino-acid residues, could be mistakenly converted into an amino-acid with a corresponding name.
The charge option
Normally, upon conversion, the atomic charges are taken from the icm.res library entries. Option charge tells the program to inherit atomic charges from the os_non-ICM-object. For small molecules, use set charge, set bond type and, possibly, build hydrogens before conversion of a new compound. i_out will contain the number of heavy atoms missing from the pdb-template.

The graphic option preserves the graphical representations and colors as is.

The selection option preserves the atom selection bit during the conversion. Useful for in-place convert.

The sstructure= tree_substructure option makes sure that the tree is drawn through the substructure. It also needs a consistent entry atom provided as as_newRoot argument.

The auto option converts in-place preserving graphics and selection information. This is a convenient shortcut for the following combination:

• graphic
• selection
• s_newObjectName is set to the input object name

Additional cleanup
Actually more procedures need to be performed to prepare a functional object from crystallographic coordinates, e.g. identifying optimal positions of added polar hydrogens, assigning the most isomeric form of histidine , and finding a correct orientation of side-chain groups for glutamine and asparagine.
We recommend the convertObject macro instead of the plain convert command to achieve those goals.
Refining the model
To refine a model use the refineModel macro.
convertObject macro
The convertObject macro is a convenient next layer on the convert command. The macro may convert only a few molecules out of your pdb file, optimize hydrogens and do some other useful improvements of the model.

Example:

read pdb "1crn"
display
as_graph = a_//c*
convert auto    # converts in-place preservinf slection and graphics
strip virtual
convert         # creates new a_1crn_1. object

If single atom is provided as an input selection it will be taken as a new ICM tree root. See convert and reroot for details.

See also:

• strip
• convertObject
• convert2Dto3D
• set cartesian

• uses all-atom residue templates (including hydrogens) from the icm.res library
• creates temporary ICM-library descriptions for unknown residues
• makes geometry identical to the PDB coordinates: bond length and bond angles may be distorted.
• the converted structure will be energy strained because of common imperfections of the PDB entries and the hydrogen atoms added by the procedure
• C-alpha-only structures will not be properly converted because a special prediction algorithm is required to extrapolate the coordinates of all atoms from C-alpha atom positions.
• these objects are good enough for graphics, skin, secondary structure assignment, rigid body docking. They are not good for loop modeling and side-chain modeling.
• needs to be followed by polar hydrogen placement and histidine state prediction ( implemented in the convertObject macro )

• you need to create a sequence file first and use the build command;
• you will need to create the missing residues manually, say, with the write library command;
• build will use all-atom residue templates including hydrogens, and will preserves the fixation;
• the linear chain with fixed idealized covalent geometry or, actually, any fixation you define, will be threaded onto the PDB coordinates in the best possible way;
• Ca-atom PDB structures will be handled properly if all backbone torsion angles are unfixed;
• the resulting ICM-object will be strained and will need further relaxation.

• uses minimize tether to create the starting conformation;
• employs a multi-step energy minimization (annealing) of the structure to relief energy strain;
• these are the best objects that can create in ICM for further simulations.

 
   read pdb "1a28.a/"           # reading just the first molecule 
   convertObject yes yes no no  # the best way to prepare for docking 
                                # convert + optimizes polar H, His and Pro 
 
   read pdb "1crn"         # X-ray object, no hydrogens, no energy parameters  
   convert                 # a_1crn_icm ICM-object will be created  
   convert a_1. "new"      # a_new. ICM-object will be created  
   convert a_1. exact      # keep modified residues as is 
 
   read mol2 s_icmhome+"ex_mol2" 
   set object a_catjuc. 
   build hydrogen  
   set type mmff 
   set charge mmff 
   convert  

If you want to create a local "epitope" of a protein with chain fragments around a particular area, it can be done with the

convert rs_fragments

command. This command will create a molecule divided into fragments and each fragment will start from virtual atoms vt1 and vt2 and will be controlled with 6 virtual variables. The first vt1 of the second, third etc. fragments will be connected to the first real atom of the first fragment. Example:

read pdb "1crn"
convert a_/4:10,12,27:33,41:45
Nof( a_m//vt1 ) # the number of pieces
show v_/P1/V  # the pos. variables of the 1st part
show v_/P2/V  # the pos. variables of the 2st part
display ribbon
color ribbon a_/P3  # showing the 3rd part

This operation is useful to create a local patch object for docking of global optimization.

Converting a chemical compound from a mol/sdf or mol2 files.

To convert a chemical from GUI menus, follow these steps:

• make sure that bond types and formal charges are correct
• select the MolMechanics.ICM-Convert.Chemical menu item, check the parameters and press OK. Normally to convert from 2D to 3D you need to optimize the ligand. ICM will perform a multiple start global optimization using the MMFF94 force field ( internally it runs the convert2Dto3D macro ). If you want to preserve the geometry, select the keepGeometry option.

 
# assuming that bond types and formal charges are correct 
build hydrogen  
set type mmff 
set charge mmff   
randomize a_//!vt* 0.01 # sometimes it helps to avoid singularities 
convert 
set v_//T3 180.  # making flat peptide bonds 
fix v_//T3       # optional 

Example of geometry optimization:

read mol input = String( Chemical( "C(C(O)=O)N1C(C(=Cc2ccc(c3ccccc3[Cl])o2)SC1=S)=O" ) )  # read 2D mol
convert2Dto3D a_ yes yes yes yes   
# Hint: if you have forgotten a macor arguments you may always type "list <macroName>"
list convert2Dto3D

auto option behaves as in normal convert command. It preserves selection and graphics and preforms in-place conversion.

If you need to reroot an ICM object, do the following:

• strip it to a non-ICM object: e.g. strip virtual
• re-root and convert, e.g. convert a_//hb1 .

Example:

build smiles "C(=CC=C(C1)C(=O)O)C=1"
display wire
wireStyle = "tree"
strip a_ virtual
convert a_//h31 auto   # converts from a new root

copy

[ copy-object ]

copy os_ [ s_newObjectName ] [delete|display|graphic|selection|stack|strip|tether]

creates a copy of os_ with the specified name. Default source object is the current object. The default name is "copy" (object a_copy. )
Options:

• delete forces the command to overwrite the object with the same name if there is a name conflict.
• display or graphic copy the display attributes of the parent
• selection copies named selections defined on the parent object into the copy
• stack copies internal stack of the object (see store-object-stack) (the stored stack is not copied by default)
• strip applies the strip operation to the copied object. The stripped object has a PDB type and is much smaller in memory.
• tether applies tethers from the source object to the atoms of the copy-object. For further refinement see the refineModel macro.

Examples:

 
 read pdb "1crn" 
 copy a_           # creates a_copy.    
 copy a_1. "aaa"   # creates a_aaa.  

 read object s_icmhome+"crn" # read ICM object 
 copy a_ strip delete tether # create a_copy. and tether to it 

 
crypt key="HeyMan" "_secretScript"    # encrypt and create *.e file 
crypt key="HeyMan" "_secretScript.e"  # decrypt it

ss="Secret rumour: Div(Rot(F))=0 !" 
crypt key="fomka" string = ss  # encrypt 
show ss 
crypt key="fomka" string = ss  # decrypt 
show ss 

Date data-type

A basic ICM class for arrays of date objects

See also: Date.

delete ICM shell objects

[ Delete shell object | delete alias | Delete molcart | Delete plot | Delete selection | Delete variable | delete atom | delete directory | delete file | Delete session | delete hydrogen | delete object | delete molecule | delete bond | delete boundary | delete conf | delete drestraint | delete label | Delete label chemical | delete link | delete map | delete sequence | delete site | delete sstructure | delete disulfide bond | delete peptide bond | delete stack | Delete stack object | Delete element | delete table | delete term | delete tether | Delete parray | Delete chemical selection ]

delete all # to delete all shell objects not marked with a no delete flag

ICM-shell objects have unique names; to delete some of them just type
delete [ mute ] { icm-shell-objectName1 | s_namePattern1 } icm-shell-objectName2 ...
You may use name patterns with wildcards (see pattern matching) and add explicit specification of the ICM-shell object type, if you want the search to match only the objects of particular type. If the ICM-shell object type is not specified, all the shell-variables will be considered.
Option mute will temporarily switch off the l_confirm flag.
delete class

delete string className

delete string command | html

to delete icm-command files or html-documents loaded into ICM

delete rarray view

to delete all the views (returned by the View() function)

Examples:

 
   delete aaa           # delete ICM-shell object aaa  
   delete a b c         # delete ICM-shell objects a, b and c  
   delete "*"           # delete ALL ICM-shell objects added by user  
   delete "mc?a*" mute  # delete ICM-shell objects matching the pattern  
   delete rarrays       # delete ALL real array  
   delete objects       # delete ALL molecular objects, same as delete a_*.  
   delete rarray "a*"   # delete real arrays starting with 'a'  

 
  a={1 2 3 4 5 6}   # we want to delete elements from it 
  a=a[2:4]          # retain only elements 2:4 
  a={1 2 3 4 5 6}    
  a=a[{2,3}//{5,6}] # retain only 4 elements elements  
  a=Count(100) 
  a=a[Count(1,10)//Count(21,30)]  # retain ranges 1:10 and 21 to 30 

 
 delete t.A>1 
 delete t[{1 3 5}] 

delete alias

delete alias
see alias delete alias_name . Example:

 
alias ls list 
alias delete ls 

Delete from database

delete molcart table s_dbtable [connection_options]

Deletes table from Molcart database with all index tables, related indexes and metadata. Database connection may be specified by connection_options

Delete plots from the table

delete plot table [name=s_handle]

This command deletes from the table all plots or only the plots with the specified name (see make plot).

ICM table plots are stored in the table header as an sarray T.plot, so 'delete plot T' is identical to 'delete T.plot'

delete selection variable

delete as_selectionName
or
delete vs_selectionName
delete named variable with atom or v_ selections. The number of named selections is limited to about 10 in each category, therefore you may need to delete them from time to time.
Important: keep in mind that deleting the named selection is not the same as deleting actual objects, molecules or atoms selected by them. To delete atoms selected by a named variable in an non-ICM object, add keyword atom (see delete atom nameSelection )
Examples:

 
 build string "ASFGD"      # build a molecule  
 vsel = v_//phi,psi    # this is a vselection  
 delete vsel 
 
 asel = a_//c*,n*      # this an aselection (atom selection)  
 delete asel           # delete variable asel, do not touch the atoms 
 delete atom asel      # delete atoms in a non-ICM object 

delete variable array {i_elementNumber|I_elementNumbers}

delete one or more elements from any array. If the array is a column in a table T, use the delete T[i] command which can delete both a single row, e.g. delete t[2], or a row selection.

Examples:

a={1 2 3}
b={1. 2. 3.}
c={"a" "b" "c"}
delete variable a 2  # deletes the 2nd element of the array
show a
 {1 3}
delete variable b 2
delete variable c 2
#
a = Count(100)
delete variable a Count(50)*2 # deletes even numbers

delete variable pairdistArray I_pos

Removes elements at positions I_pos from the array

delete atom

delete as_atoms

delete atoms as_namedSelection
delete selected atoms in a non-ICM object. The selection here must be a constant atom selection, rather than a named selection (e.g. you can say delete a_/1:10/* but NOT aaa = a_/1:10/* , delete aaa ).
To delete a named variable, use delete atom name Example:

 
  read pdb "1crn" 
  delete a_/1:10/*   
 
  aaa = a_/18:20 
  delete atom aaa 

 
delete directory "/home/doe/temp/" 

delete system s_fileName s_fileName ...

delete file.

Example:

delete system "/tmp/aaa"

See also: delete directory rename file make directory, set directory, Path(directory)

delete history lines

delete session
deletes all previous history lines. Example:

 
call _macro 
delete session 

 
   delete object          # delete ALL molecular objects 
   delete a_*.            # delete ALL molecular objects  
   delete a_2,4.          # delete objects number 2 and 4  
   delete a_2a*.          # delete objects with names starting from 2a  
 
   read pdb "1crn"        # load crambin  
   convert                # create the second object named 1crn_icm  
                          # from the pdb object  
   delete a_1.            # delete the 1st pdb-object  
   delete Object( as_graph )  # graphical selection  

 
   read pdb "2ins"        # load insulin with water molecules  
   delete a_2ins.w*       # delete water molecules  
   delete atoms as_graph  # deletes selected non-ICM atoms/molecules 
   delete Mol( as_graph )  # deletes selected non-ICM atoms/molecules 

 
   read pdb "newmol"              # automatic bond determination is not perfect  
   delete bond a_/3/cg1 a_/5/ce2  # disconnect two carbon atoms  

delete conf i_confNumberFrom i_confNumberTo [os_obj]

delete conf I_stackConfNumbers [os_obj]
delete a specified conformation from the stack or a series of conformations starting from i_stackConfNumber to i_stackConfNumberTo . An integer array of indices can also be provided.

if the os_obj argument is provided the changes above will be applied to the local stack in the object.

 
   delete drestraint a_mol1 a_mol2       # intermolecular restraints  

 
   delete label 1  # delete the first displayed label  

delete label chemarray [index=I_]

Deletes atom annotation in 2D chemical spreadsheet.

delete link

delete link ms_

delete links to sequences and alignments for selected molecules

delete link variable

delete all groups of linked variables (e.g. unlink the variables), see also link variables .

delete map

*delete { *map | s_mapName } delete s_mapName or all maps.

• selection : delete the sequences selected through GUI.
• unknown : delete the sequences unknown to the alignments, i.e. freely floating sequence not included in any alignments.

• no arguments: delete all ICM-sequences
• one integer argument: delete last i_NofLastSequences sequences
• two integer argument: delete sequences shorter than i_minLength or longer i_maxLength

delete alignmentName only selection

delete alignmentName only seq1 seq2 ...

To delete sequences selected via the graphics user interface from an alignment without deleting them from the shell. Example

 
  delete sh3 only Fyn 
  delete sh3 only selection 

delete site ms1_ [{s_Site|i_number|I_numbers|pattern=s_}]

delete site rs_
delete the sites of the selected molecules. The sites can be specified by their name, or number, or residue selection. All sites are deleted by default.
Example:

 
   nice "1as6"          # has 3 sites, one in each molecule.  
   delete site a_1.1 {1} 
   delete sites         # delete all of them 

 
           # SS-bond specified by residue, or  
   delete disulfide bond a_/15 a_/29         
           # by atoms 
   delete disulfide bond a_/15/sg a_/29/sg   
           # remove all SS-bonds in the current object 
   delete disulfide bond all                 

 
   delete peptide bond a_/15/c a_/29/n  

delete conformational stack inside an object

delete stack os

deletes the compressed stack inside the specified object.

See also:

• store stack object
• load stack object
• montecarlo .. store
• set object .. stack
• Exist ( os1 stack )

delete parray elements

delete parray[i_index]

delete parray[I_index_list]

deletes specified elements from a parray.

Example:

C = Chemical({"C","CC","CCC","CCCC","CCCCC"})
delete C[{1,3,5}]
delete C[1]

 
   group table t {1 2 3} "a" {4. 5. 7.} "b"   
   delete t.a == 2       # the second entry  
   show t 
   delete t[2]           # the second entry  
   show t 
   delete t              # the whole thing  
   group table t {1 2 3} "a" {4. 5. 7.} "b"   
   delete t.a > 1          # 2nd and 3rd

 
   delete terms "tz,sf"    # do not consider tethers and solvation contributions  

delete tethers of the specified atoms ( as_ ), if no selection is specified all tethers in the current object are deleted.

delete tether loop [ as_] - this tool deletes tethers for residues flanking insertions and deletions (one residue on each side), as well as N- and C- termini. The tool is used to help the minimize tether command to build a more relaxed loop or end.

delete a tree from a table header array

delete variable treeParray i_treeIndex

deletes a tree object (generically considered as a parray )

Example:

make tree T  
delete variable T.cluster 1

delete chemical chemarray

deletes selected parts of the chemicals. See select chemical command.

display

[ display model | Display new | Display offscreen | display origin | Display rotate | display stack | display box | display clash | display drestraint | display gradient | display grob | Display grob label | display hbond | Hbond color | display label | display map | Display trajectory | display ribbon | display site | Display skin | display slide | display string | display tethers | display volume | display window | Display gui ]

display [transparent] [stick|skin|ribbon [base]] [as_ [as_2]]
display specified graphics primitives for selected atoms or residues.

Once something is displayed and your cursor is in the graphics window you may rotate, translate, zoom and move both clipping planes with the mouse and keystrokes.
To refer to the base part of DNA/RNA represented as ribbon , use the additional specifier called base, which can be separately displayed and colored. E.g.

 
 makeDnaRna "ACTG" "mydna" yes yes "dna" 
 display ribbon  
 color ribbon base a_1 blue 

 
read pdb "1crn" 
display transparent ribbon 
display skin transparent 

 
 build string "AFSGDH;QWRTEY"       # two peptides 
 display                        # display current object and color atoms   
                                # according to atom type  
 display a_1 red                # display the first molecule and color it red  
 display skin a_/5 a_* yellow   # display skin of the 5th residue  
                                # as surrounded by all the atoms  
 display ribbon                 # display ribbon for all the residues  
 
 read pdb "2drp"                # a pdb file 
 assign sstructure a_a/123:134,153:165 "H"       # No sstructure in 2drp  
 assign sstructure a_a/109:114,117:121,141:144,147:151 "E" 
 display a_a ribbon red                          # two Zn-fingers  
 display a_a/113,116,143,146/!n,c,o xstick blue  # Cys residues  
 display a_a/129,134,159,164/!n,c,o xstick navy  # His residues  
 display a_m,m2 cpk magenta                       # Zn-atoms   
 adna1=a_b//p,c3['],c4['],c5['],o3['],o5[']      # two DNA chains   
 adna2=a_c//p,c3['],c4['],c5['],o3['],o5['] 
 display adna1 xstick white 
 display adna2 xstick aquamarine 
 display adna1 adna1 surface white 
 display adna2 adna2 surface aquamarine 
 center 
 display "Zn-finger peptides complexed with DNA" pink 
 
# display 4 chains of insulin as 4 thick worms colored from N-to C-terminus 
 read pdb "2ins" 
 color background blue 
 assign sstructure a_/* "_"  # thick worm representation 
 GRAPHICS.wormRadius= 0.9 
 display a_/* ribbon only 
 color a_1/* Count(1 Nof(a_1/* )) ribbon 
 color a_2/* Count(1 Nof(a_2/* )) ribbon 
 color a_3/* Count(1 Nof(a_3/* )) ribbon 
 color a_4/* Count(1 Nof(a_4/* )) ribbon 
 
# examples of DNA and RNA ribbons 
 nice "4tna" 
 resLabelStyle = "A" 
 display residue label 
 color residue label a_/?u gold # ??u also selects modified Us 
 color residue label a_/?a red 

display new

display restore

display restore plane

commands to mimic some of the interactive controls. These commands are primarily used in GUI commands ( see icm.gui file) and scripts/macros.
new : rebuilds some graphical representations (e.g. your as_graph has been changed in the shell and you need to refresh the image, or you changed the orientation and want to redisplay the labels elevated above the skin surface by resLabelShift ).
restore : a softer action than new .
restore plane : moves the clipping planes beyond the displayed objects (keystroke: Ctrl-U, or the 'Unclip' button) .

 
   display off 400 300 
   nice "1est" 
   rotate view Rot( {0. 1. 1.} 50.) 
   write image "est1" 
   unix xv est1.tif 
   set window 700 800  # NB: 'center all' will be applied 
   write image "est2" 
   unix xv est2.tif 
   display a_/4/o cpk 
   center a_/3,4 
   write image "est3" rgb 
   unix xv est3.rgb 
   build string "se ala trp" 
   display off 400 300 
   display skin 
   write image "est3" rgb delete 
   unix xv est3.rgb 

 
 read pdb "1crn" 
 display 
 display origin 
 undisplay origin 

Setting rotation or rocking mode

display rotate [on|off] [ i_NofCycles ] [pause]

The graphics view can be set so that molecule is continuously rotating or rocking, but the ICM session remains interactive. This mode can be set with the above command. The style of continuous interruptable movement is controlled with the GRAPHICS.rocking preference. Specifying the number of rotation or rocking cycles i_NofCycles is useful for movie making. The pause option forces the command to finish the requested number of rotations before proceeding to the next commands, as opposed to just launching the rotation and proceeding with the rest of the script.

Example:

GRAPHICS.rocking = "xY-rocking"
display rotate on 3 # three cycles

See also: write movie , GRAPHICS.rocking

display stack

display stack [ os_withStoredStack ] [iFrom iTo] [loop [=nCycles]] [r_NofInterpolationFrames [simple|cartesian]] [center] [sstructure] [auto]

interpolated display of conformational stack of its parts. Aruments and options:

• optional os_withStoredStack . If this argument is missing, the global stack will be used. With the argument the built-in local object stack will be played out.
• optional start and end frames: iFrom iTo
• option loop [ = nCycles ] : the command makes a video loop and repeats it 99999 times. Optional nCycles redefines the number of repetitions.
• r_NofInterpolationFrames [ simple | cartesian ] ] (e.g. 10.0 cartesian ) : determines the number of intermediate frames. The following interpolations are currently provided:
  • simple : just wait for the specified number of frames
  • cartesian : perform linear interpolation between stack conformations
  The default interpolation is simple .
• option center : centers on the displayed atoms
• option sstructure : recomputes secondary structure for each stack conformation.
• option auto : extracts the number of cycles (1 or endless loop) and the number of interpolated frames ( no interpolation or a fixed number of interpolated frames) from the stack itself. The two parameters can be set with the set stack os loop|fast [off] command. The GUI interface for the object stack display uses the auto option.

Example:

  build string "ASDFW"
  montecarlo v_//x* mncalls=10 vwMethod=2 # create a conformational stack
  display xstick cpk  only
# the previous commands just prepare stack and display
  display stack 20. cartesian loop=4 center # repeat 4 times and stop

# make the same preparations
  write movie "peptamovie" on exact
  display stack 20. cartesian loop=1 center # repeat 4 times and stop
  write movie exit

The display stack command is somewhat similar to the display trajectory command. The display stack command has the following benefits:

• it recomputes the skin if the skin is present
• does not mess up the C-terminus in case of local deformations
• does not save or use any external files.
• it allows easy looping with the loop [= nCycles ] option.

See also:

• display trajectory
• write movie
• store frame
• stack

display box

display box [ R_6boxCorners ]
display graphics box specified by x,y,z coordinates of two opposite corners of a parallelepiped. This box can be resized and translated interactively with the Left and Middle mouse buttons:

• Resizing: Grab a corner of the box with the Left-Mouse-Button and drag it to resize the box
• Translating: Grab a corner or a center of the box with the Middle-Mouse-Button and translate

See also the Box () function which returns six parameters describing the box.
Examples:

 
   build string "se ala his gly met" # a peptide  
   display 
   display box                      # the default box   
   display box {0. 0. 0. 2. 2. 2.}  # define position/size 
   display box Box(a_/2 )           # surround the a_/2 by a box  
   display box Box(a_/2 1.2)        # or add 1.2A margin 

display clash

display clash [ as_1 ] [ r_clashThreshold ]
display all the interatomic distances for selected atoms which are shorter than the sum of van der Waals radii multiplied by the r_clashThreshold parameter. The default value is taken from the clashThreshold variable. Initially it is set to 0.82 but can be redefined. IMPORTANT: this will work only for the ICM-objects. For hydrogen bonded atoms the threshold is additionally multiplied by 0.8. Use the show energy "vw" command (and pay attention to the current fixation) to precalculate interaction lists.
This command may show some irrelevant short contacts. calcEnergyStrain , display gradient , etc. seem to be more informative.
See also: GRAPHICS.clashWidth , clashThreshold , show clash, undisplay and atom energy gradient (force) analysis with: show a_//G or display a_//G.
Example:

 
 read object s_icmhome+"crn" 
 show energy "vw" 
 display a_
 display clash                  # all clashes, default clashThreshold=0.82
 undisplay clash 
 display clash a_/11 0.95  	# distances < (R1+R2)*0.95  
# this is an alternative method which analyzes the gradient 
 selectMinGrad = 100.   	# analyzes forces greater than 100 
 display ribbon grey 
 display Res( a_//G )  
 display gradient a_//G 
 color Res( a_//G ) ribbon magenta    

 
  build string "se ala his trp ala gly gly" 
  display 
  set drestraint a_/1/hn a_def.a1/6/o 2  
  show energy "cn"
  display drestraint 
  minimize "vw,14,to,cn" 

 
 build string "ala his trp glu leu" 
 randomize v_//phi,psi 
 show energy 
 selectMinGrad= 20.
 display a_ 
 display gradient a_//G 

• dot will show only dot-vertices of the object.
• reverse to invert lighting; this option will change directions of the grob surface normals (will turn the grob inside-out)
• smooth enforces the Gouraud shading method to smooth the solid surface.
• solid allows solid surface representation of the object and requires that the original object has information about triangles forming the solid surface.
• transparent makes solid grob transparent

 
   read matrix s_icmhome+"def.mat"    	# 2D sin(r^2)/r^2 function of a grid 
   make grob solid def      		# convert matrix into a graphics object g_def 
   display g_def smooth     		# a hat of the 22st century  
   rotate view Rot({1. 0. 0.}, 45.)     #  
   display g_def reverse    		# shine light from inside the head 
   display grob smooth transparent 	# like Lenin in Mausoleum  

set font of a 3D label

display g_label [bold ] [ italic ] [ underline ] i_Size [font=s_FontName] [rgb=R_3rgb|"#xxyyzz"]

displays g_label text (technically it is a grob with a single point and associated text) in a particular font.

Example:

read pdb "1crn"
display a_
label3d = Grob("label",Mean(Xyz(a_/3,4)), "3D label for res 3,4")
set font label3d times 36 rgb="#00ffdd"
display label3d
select edit label3d # makes it movable, press Esc to get rid of the cursor

The color or hydrogen bonds will be calculated according to a calculation involving the effective lone pair density (see hbond color ).

See also: undisplay hbonds, show hbonds.

Strength and color of a hydrogen bond

The hydrogen bonds created or displayed with the make hbond or display hbond commands are colored according to the estimated 'strength' of this hydrogen bond. This is just an estimate since the energy of hydrogen bond is not easily decoupled from the van der Waals and electrostatic contributions between the hbonded atoms and their immediate environment. In ICM the strength is estimated using the following procedure described in J Med Chem. 2003 Jul 3;46(14):3045-59.

For a hydrogen bond acceptor atom A(i) and a hydrogen atom H(j) located at r_j, the hydrogen bonding interaction was estimated

F_{ang(phi)Fdist} (r_LPi -r_j)

, where phi is an angle formed by the hydrogen bond acceptor atom, hydrogen, and the hydrogen bond donor, and r_LPi is the radius vector of the center of the lone electron pair (LP) closest to the hydrogen. The angular function used was defined as F_ang = 1 - cos(k*phi) . Parameter k is accessible as GRAPHICS.hbondAngleSharpness in the shell. Distance function F_dist (r_LPi-rj) was constant (1.0) within L_HB/2 from the lone pair center and dropped as

exp( -(((r_LPi - r_j)/LHB) - 0.5)² ) .

beyond that distance, where L_HB is the characteristic range of hydrogen bonding interaction (value of L=1.6 �was used). Lone pair centers were placed at 1 �from the hydrogen bond acceptor atom, assuming symmetrical planar trigonal configuration for sp2 atoms and tetrahedral configuration for sp3 atoms. The resulting functional dependence reflects (at least qualitatively) the physical nature and observed statistics of the hydrogen bond interactions. The interaction is maximized when the hydrogen atom is pointing directly to the acceptor atom along a lone pair axis and drops quickly as the hydrogen is moved farther away. The strength declines more gradually as the hydrogen moves out of the LP axis or, as hydrogen bond donor, hydrogen atom, or hydrogen bond acceptor, move out of alignment.

See also: GRAPHICS.hbondMinStrength

display label

display [{ atom | residue }] label [selection]
display variable label v_selection
a graphics label with atom name, residue name, variable name for all or selected atoms, residues or variables respectively. The text of this label is not user-defined, although you can control it in two different ways. First, residue label style can be set using either Ctrl-L in the graphics window or resLabelStyle preference , and variable label style either by Ctrl-V, or setting varLabelStyle preference. Second, the ICM-shell string variable s_labelHeader defines a prefix string for all labels. For example, if you display CPK atoms you may move the label to the right from the atom center by s_labelHeader=" " .
The _aliases file has convenient aliases (e.g. ds for display, unds for undisplay, re , for residue, va for variable) for those of us who like typing commands. In this case you may just type ds va la to display variable labels, etc.
Examples:

 
 build string "FAHSGDH" 
 display a_
 display residue label #  
 undisplay label 
 display residue label a_/his 
 display variable label v_//phi,psi 
 display variable label v_//* & as_graph 
 display atom label a_/1:3/* 
 undisplay label 
# or with aliases: 
 ds re la a_/1,3 
 unds la 
 .. etc. 

• 0 - transparent/invisible
• 1 - blue
• maxNumer - red

 
   build string "se his arg"  
   make map potential "el"  Box( a_/1,2/* , 3. )  
   display a_ 
   display map m_el {1 2 0 0 0 0 3 4 5 6} {-20.,100.}
   center
   make grob m_el 2. name="g_1"
   make grob -m_el 1. name= "g_2"  
   display g_1 red 
   display g_2 blue 

Arguments and options:

• Integers i_From and i_To specify the frame range.
• Real values r_Smooth1 and r_Smooth2 determine minimum and maximum smoothing parameters (i.e. number of additional frames, inserted if conformation change is too dramatic). For example: 100. 700.
• Specifying atom selection as_1 defines a certain fragment on to the initial conformation, of which subsequent conformations are superimposed.
• The image saving options include: image [ =s_framePath ] [ rgb|targa|png|gif ] Option image allows to automatically save a series of image files in the s_framePath argument of the image= option or in the default s_tempDir directory.
• center option with selection as_2 determines a fragment for graphics window centering (all, if center without as_2 ).

To obtain the trajectory info use
read trajectory s_TrjFileName
When playing a trajectory, you can use ICM interrupt ( Ctrl-\ ) to stop, and then toggle stepwise frame playing, reverse, or quit playing. The default is to play a whole trajectory without smoothing, superimposition or centering. Example:

 build string "ala ser ala thr ala glu ala"
 mncallsMC=10000                         # 
 montecarlo trajectory
 read trajectory "def"
 ds ribbon, wire
 ds trajectory center sstructure  10.

• do not forget to start ICM with the -24 flag to double the image quality.
• set IMAGE.generateAlpha to no if you want to keep the background colored and not transparent.

Allowed image formats are: rgb, targa, png, gif . The file extensions will correspond to the image file format. The image file names consist of the default path and name, appended with the frame number. Example:

 
 display trajectory image="/tmp/f"  
 /tmp/f_1.png 
 /tmp/f_2.png 
 ... 
 s_tempDir = "/home/jack/X" 
 display trajectory image rgb 
 /home/jack/X_1.rgb 
 /home/jack/X_2.rgb 
 ... 

display ribbon rs_ color

displays protein or DNA backbones in ribbon presentation.

See also:

• ribbon
• undisplay

display { skin | surface } as_1 as_2

display skin as_1 molecule
display analytical molecular surface, also referred to as skin, or solvent accessible surface area . Each display skin command will delete the previously displayed skin in the current plane. To display several different skins, use the set plane command to change the current graphics plane before you issue the display skin command. You can also convert the skin into a grob with the make grob skin command. You can co-display many grobs on the same plane, as well as make the grob transparent. This grob can be further split into individual shells with the split command.

Options:

• molecule : (for skin) considers each molecule in isolation

See also: How to display and characterize protein cavities.
Example:

 
   build string "se ala his glu"  # test tripeptide  
   display                        # the wire model  
   display skin a_/1 a_/1         # skin around the 1st residue or just press <F1> 
   display skin a_1 molecule      # equivalent to a_1 a_1
   set plane move on 2            # key with your cursor in the graphics window 
   display skin a_/3 a_/3         # skin around the 3st residue 
                                  # now you can toggle planes with F2 and F1 
   display surface                # solvent-accessible surface 

display slide [ reverse | i_slide ] [s_slideProperties] [ view ] [ smooth ] [ add ] ]

display the next slide or slide number i_slide . Options:

• which slide to show? if you have just said: display slide the next slide will be shown, display slide reverse will show the previous one. A specific slide number i_slide can also be shown ( ICM also understands index=3 ).
• view : using only the viewpoint/clipping planes from a slide (see also set view ).
• smooth : or smooth= i_transition_time_in_msec will make a smooth view transition from the current state to the slide view. (e.g. display slide smooth or display slide 5 smooth=1000
• add : adding representations to the existing display, rather than overwriting the slide (like appending a new graphical layer)

You can individuall control which sections of the slide information to use in display slide using s_slideProperties . The syntax of this string is the following: "sect1on;sect2on;..;-sect3off;sect4off; .." The section names are separated by a semicolon, and plus and minus are used to switch things on and off with respect to the default state. The allowed sections include:

Section Name	Default	Description
"layout"	-	if +, sets the layout of ICM windows and panels (if off, preserves the current layout)
"activewindows"	+	if +, sets the saved active window or panel in ICM gui
"smooth"	-	if +, makes smooth animated view transitions between slides
"add"	-	if +, adds the next slide as a layer to the previous, rather than overwrites it
"gf"	+	graphical representations (CPK, xstick, skin etc.)
"color"	+	colors of representations
"labeloffs"	+	restoring slide-specific displacements of residue labels
"viewpoint"	+	the view point, zoom, and clipping planes
"graphopt"	+	the state and parameters of rotation, rocking, etc.
"mol"	+	if - , do not restore any property of molecular objects in main graphics window
"grob"	+	if - , do not restore any property of grobs in main graphics window
"map"	+	if - , do not restore any property of maps in main graphics window
"all"	-	switches all sections, on (+) or off (-)

Examples:

 display slide 4 "-all;+gf;+color"
 display slide 4 "-viewpoint"
 display slide 4 "+smooth" # enforce smooth view transitions

display slide show [ index=i_start ] [reverse]

the keyword show switches the program into the slideshow mode and makes smooth transition the default. Other options are the same as above.

Examples :

icm -g&
read binary s_icmhome+"example_slideSGC.icb"
display slide
display slide # the next slide
display slide smooth # make a 500msec-transition 
display slide 4 # 5th slide 
display slide 2 view  # enforce viewpoint from slide 7
display slide add 2 # display additional representations from slide 3

See also: add slide , set view .

display string

display string s_StringText [color_spec] [font_spec] [ r_XscreenPosition r_YscreenPosition ]

display a text string in the graphics window. Relative X and Y screen coordinates (ranging from -1. to 1.) of the string beginning may be specified to display the string in a given location. Defaults are x = -0.9, y = 0.9, i.e. upper left corner of the screen.

The string can be dragged later to any location by the middle mouse button.

The command supports various formats for specifying the label color color_spec and font parameters to characterize the label font font_spec.

Two fonts are at your disposal: the default font (usually times) and the auxiliary font (usually symbol). Both fonts can be redefined by the set font command. You can also switch to the auxiliary font and back inside the string by backslash-A ( \A). (.e.g "Red: \Aa\A-helix"). You can also list and delete your string labels by the list label and delete label commands.
Examples:

 
display string "Crambin"                            # a simple string  
 
display string "Act.site of \Ab\A-lactamase" yellow # Greek beta letter  
 
build string "ala" 
display string Name(a_1.) red 28, 0. 0.9     # first object name  
                                             # in the middle  
                                             # (font size=28)  

display volume

activates fog from the command line. See also fogStart . Accordingly, the undisplay volume switches the effect off.

display window

display window [ i_xLeft i_yDown i_xSize i_ySize ]

undisplay window

displays/undisplays the graphics window. When ICM is started without GUI, it is allowed to specify the window size and position.

See also: set window

display window=s_windowList

undisplay window=s_windowList

Displays/undisplays GUI windows and toolbars. s_windowList should be a comma-separated list with ICM panel and toolbar names.

• "opengl" # undisplays the graphics window
• "all" # undisplays all except graphics window
• "alignments"
• "htmls"
• "masterview" # shows/hides workspace panel
• "moledit" # shows/hides molecular editor window
• "plotdialog" # shows plot dialog for the current table (in modal mode)
• "searchwindow" # show/hides chemical search space window. Chemical pattern can be provided optionally as an extra argument
• "columnfilter" # launches column filter dialog for specified table column
• "tablesearch" # launches table "Find and Replace" for the active table. Search string can be provided optionally as an extra argument
• "processes" # shows/hides background job list window
• "prop" # 'Display Panel' with mutiple tabs (display/light,...)
• "terminal"
• "tables"

• "moveTools"
• "clipTools"
• "miscTools"
• "viewTools"
• "planeTools"
• "fileTools"
• "levelTools"
• "tableTools"

You can also display/undisplay individual tabs from the 'Display Panel'. To do that you need to append a tab name to the "prop:".

Example:

undisplay window="prop:light"   # hide 'light' tab from the panel

Note: This command does not affect the content of the main working area (the center)

Example:

read binary s_icmhome + "example_search.icb"
display a_
undisplay window="tables" # hides tables 
undisplay window="all"    # leaves only 3D graphics window
display window="moledit" Chemical("CCO")  # popups Molecular Editor with compound
display window="searchwindow" Chemical("CC[O;D1]")  # popups Chemical Search Space with compound

display window=s_window center

sets the specified s_window to the center. Windows which may occupy the central position are:

• "opengl"
• "alignments"
• "htmls"
• "tables"

Example:

read binary s_icmhome + "example_search.icb"
display a_
display window="opengl" center # sets graphics window to the center

display window=s_layoutString

Applies the window layout specified in the s_layoutString. ICM stores the layout information as a string in a specific format. Window layout information is stored, for example, in slides.

Example:

read binary s_icmhome + "example_search.icb"
sl = Slide()
display a_
display window=String(sl gui) #changes the view back to what was before the 'display' command

See also: Slide, String slide gui

display GUI windows

display gui [off] s_window

Obsolete command. See: display window

 
   edit mncalls   # actually it is easier to type: mncalls=333 
   edit FILTER    # edit a system table, do not change names of components 
# 
  group table t {1,2,3} "A" {"a","b","c"} "B"  	# create a table
  t						#
  edit t					# edit table t 

 
   macro threeEssentialsOfLife          # declare new macro  
                                        # define essentials  
      l_info=no 
      modes={"\n\tOoops!!\n","\n\tOuch!!\n","\n\tWow!!\n"} 
                                        # randomly pick a line  
      print modes[Random(1,3)] 
   endmacro 
   threeEssentialsOfLife                # invoke macro  

enumerate chiral chem_array [index=I_selectedChems] [center=i_Max_Number_of_Centers] [name=s]

Generates all possible stereo isomers for each chemical compound from or from selected chemicals ( I_selectedChems ). Important: this operation requires that two conditions are satisfied:

• a molecule has a stereo center (i.e. an sp3 atom with four different substituents
• if a stereo center has a definite chirality ( "up" or "down", or R, or S) stereo isomers will not be generated. The center needs a stereo bond is marked by type "off", or "either" to imply an uncertain chirality or a racemic mixture of two isomers.

Sometimes you may want to skip compounds with number of unspecified centers greater than certain value. In this case you should provide center = i_Max_Number_of_Centers argument to the command.

The command will always generate at least one element for each compound. Example:

group table t {"CC(N)O","CC(C)C(C)O"} "mol"
enumerate chiral t.mol name="isomers" # creates isomers.mol

Tautomer enumeration

enumerate tautomer chem_array [keep] [filter] [index=I_index_array] [name='T_tauto']
Generates all possible tautomers for each chemical compound from . Returns the resulting chemical array of tautomers. The command will always generate at least one element for each compound.

The current function only generates tautomers that preserve the atom content (does not add or remove hydrogens). With keep option it'll also preserve the hybridization state of each atom (i.e. does not change sp3 to sp2).

Some tautomers are formally possible but chemically do not make much sense. To avoid generating those tautomers, Split uses the TAUTOFILTER.tab file that contains the unwanted or chemically impossible tautomer patterns in the SMARTS format. Feel free to add more patterns to this file. Use filter option to enable filtering by patterns.

Example file:

#>T TAUTOFILTER
#>-sm----------------comment
"*C([OH1])=[N;R0]"  "peptide bond"

 
 p = Chemical( "C(=C(NC(=N1)N)N2)(C1=O)N=C2" )
 Nof(p) # 1 element 
 1 
 enumerate tautomer p
 show T_tauto
#>T T_tauto
#>-mol---------idx--------
  "C1=NC2=C(NC(=N)NC2=N1)O" 0
  "c1nc2=C(NC(=N)N=c2[nH]1)O" 0
  "C1=NC2=C(N=C(N)NC2=N1)O" 0
  "c1nc2c(nc(N)nc2[nH]1)O" 0
  "C1=NC2=C(NC(N)=NC2=N1)O" 0
  "c1nc2C(NC(=N)Nc2[nH]1)=O" 0
  "c1nc2C(N=C(N)Nc2[nH]1)=O" 0
  "c1nc2C(NC(N)=Nc2[nH]1)=O" 0
  "c1nc2C(=NC(=N)Nc2[nH]1)O" 0

Combinatorial library enumeration

enumerate library [simple] chem_scaffold_R1R2 .. chem_R1 chem_R2 .. \ [name= s_libTableName|output= s_fileName] [filter=expression]

Applies chemical arrays (usually a column in a chemical table) for each of replacement groups chem_R1, chem_R2 etc. to the first element of the scaffold template array. (also known as enumerate library

The scaffold.The scaffold structure needs to be drawn as a Markush structure, e.g.

add column scaffld Parray( "[R2]C(C(=O)[R3])NC(=O)N[R1]" ) name="mol"

The replacement groups.Each replacement group in a chemical array (table) needs to have an attachment point specified. In the Smiles/Smart representation used in ICM it is marked by an asterisk (e.g. "[C*]CC" ). Marking an atom as an attachment point can also be done in the Chemical Editor ( right-click on an atom and choose the Attachment Point menu item).

The output table or file.The output table will contain all combinations . If the output option is specified the resulting library is saved to a file and the table is not created. Warning: if the number of combination exceeds 20000 the resulting library is saved to a file automatically (to avoid memory problems).

• Option name = s_table allows to change the default name of the output table.
• Option output = s_file forces the file output and suppressed the table creation.

The output chemical table has a product column as well as the index of each R-group.

simple option toggle a special mode where instead of full enumeration it simply goes through the input substituents and take i-th element from each. This mode requires that size of all R-group arrays should be the same. The size of the output will be equal to the size of R-group array(s)

Dynamic filtering of the output by applying a filter expression.The filter= s_expression option allows to apply a filter during the library generation. The filter expression is a double-quoted string with the following structure: "Function1 relation value & or | Function2 relation value & or | .. "

Example:

filter = "MolLogP<5. & Nof_Frags('C(O)=O')<1"

The list of functions is expanding. The current list of the functions is the following:

Function Name	Description	Example
MolWeight		MolWeight < 650
Nof_Molecules	the number of individual molecules,including ions and salts	Nof_Molecules==1
Nof_Chirals	the total number of racemic and chiral centers	Nof_Chirals==0
Nof_RotB	rotatable bonds
Nof_HBA	hydrogen bonding acceptors
Nof_HBD	hydrogen bonding donors
Nof_Atoms	the total number of non-hydrogen atoms
Nof_Frags ( s_smart )	counts the number of fragments	Nof_Frags('[S,P](=O)=O')==1
DrugLikeness	a number around 0	DrugLikeness > 0
MolLogP	log P prediction
Volume	3D molecule volume prediction
MolPSA	polar surface area
MoldHf	heats of formation
MolLogS	solubility

See also:

• Predict for a detailed description of some of the functions.
• make reaction

A short form of the enumerate library command and linking. The replacement group arrays can be linked to the R positions of a scaffold with the link group command. In this case a short form of the command can be used, e.g.

link group scaffold.mol 1 r1.mol 2 r2.mol 3 r3.mol
enumerate library scaffold.mol

Example:

 read binary "example_enum.icb" # contains scaffold and R1,R2,R3
 enumerate library scaffold.mol[1] name=Name( "lib", unique ) R1.mol,R2.mol,R3.mol
 split group scaffold.mol[1] lib.mol   # if you want to split it back

The inverse operation: split the library into scaffold and replacement group arrays.A library can be also reduced back to the scaffold and replacement groups using the split group scaffold library command. E.g. split group scaffld.mol combilib.mol

See also: make reaction , split group , Replace chemical .

endwhile

endwhile
is one of the ICM flow control statements, used to perform a loop in ICM-shell calculations. See also while .

[ Find alignment | Find database | Find database fast | Find molecule | Find chemical | Find pdb | Find prosite | find pattern | Find molcart | Find table | Find pharmacophore ]

• find pdb: search a database of a single structure for a fragment with a given sequence pattern and partial structural similarity (e.g. loop ends match).
• superimpose: performs structural superposition, the command can do it on the basis of sequence alignment on the fly.

 
 read pdb "1nfp" 
 read pdb "1brl.b/" 
 rm !Mol(a_*./A ) 
 make sequences a_*. 
 aa=Align(1brl_1_b 1nfp_a) 
 ds a_1.//ca,c,n grey 
 ds a_2.//ca,c,n green 
 superimpose a_1.1 a_2.1 aa 
 center 
 find aa superimpose 
 show aa 
 
 gapExtension = 0.05 
 ab=Align(1brl_1_b 1nfp_a) 
 find ab 4. 0.7 superimpose 
 show ab                         # better 

See also: pairwise alignment multiple alignment

find database exact [ distance= i_nOfMutations]] options

find database pattern={ s_pattern | S_patterns } options

find database write [ s_database ]

find database fast [ = i_speed] [output=s_file] [name=s_tabName] # blast like fast search.
fast sequence or pattern search through a sequence database.
The default find database sequence search program performs a full gapped optimal sequence alignment, which is a global alignment with zero-end-gap penalties (ZEGA). These alignments are more rigorous (not heuristic) than popular BLAST of FASTA searches. The latest statistics of structural significance of sequence alignments derived for a number of residue substitution matrices will be applied ( Abagyan and Batalov, 1997 ) to assess the probability that a matching fragment shares the same 3D fold. The r_probabilityThreshold (default 0.00001 or 5.) option defines the lowest acceptable probability of hit. You can also provide a -logP number (e.g. 5.5 ) instead of a small probability ( 10^-5 ). Threshold of 10/DatabaseSize is usually a safe threshold (no guarantees though). Practically 10^-5 is a safe threshold for a SWISSPROT search (65,000 sequences). At 10^-4 you may find interesting hits, but a more serious analysis may be required to confirm its significance.
The second version of the command with the exact keyword performs a very fast search for identical or almost identical sequences. The distance= i_maxNofMutations parameter specifies the allowed number of mutations.
find database pattern

The third version of the command searches for string patterns in a sequence database. The sequence patterns can contain while cards (e.g. "A?[LIV]?\{3,5\}[!P]"). This search is very fast.
The fourth command find database write is used to export ALL sequences from the blast-formatted files into to an external FASTA file defined by output= string (default s_databasePath.seq ). This option is the inverse of the write index sequence command which creates several BLAST files from a FASTA file.
The common options are as follows: [ s_databasePath ("pdbseq") ] [ seq_1 .. ] [ ali_1 .. ] [ output= s_outputFileNameRoot ] [ name= s_tableName ] [ unique ] [ delete ] [ protein | nucleotide | type ]

• DATABASE: s_databasePath (default: "pdbseq" files in the $BLASTDB directory) defines the path of the three files with the compressed sequence files. For compatibility these three files (.bsq, .atb, .ahd) are the same as generated by the setdb (BLAST) command. The available files can be vied with the list database command, by default the "swiss" file is taken from the $BLASTDB directory. If the environment variable $BLASTDB is set, the three files will be taken from this directory. To read database files from any directory, specify its explicit path (e.g. "./myLocalDb" or "/home/user/myHomeDb1") Note: when the PDB sequences are updated, the blast files go into s_userDir + "/blastdb" , On Linux the database is at "~/.icm/blastdb/pdbseq" . To make this directory the default blast directory, reset the s_blastdbDir to "/your_home/.icm/blastdb/". In GUI, choose File;Preferences;Directories and modify the s_blastdbDir variable.
• QUERY: seq_1 .. (list of sequences), or ali_1 .. (list of alignments), or keyword selection determines which sequences will be searched against the database. The default (no argument) means that all the sequences currently present in the ICM-shell (see list sequence) will be searched. The selection can be made from the ICM GUI.
• OUTPUT FILES: option output= s_projName to redefine the name of the project. The default name of the output files is the name root of the database file. The following files are saved

   
   projName_seq  # query sequence(s) 
   projName.seq  # a sorted list of database sequences truncated to the matching fragment. 
   projName.tab  # the result table 
  

• TABLE: option name= s_resultTableName defines the names of output table which is created after the search. The table contains the boundaries of the hits, sequence identities etc.
• option margin= i_seqMargin in the pattern search defines the length of flanking sequences added to the matching fragment and saved in the s_projectName.seq file for further retrieval. Specify a very large number to store complete sequences.
• option delete will overwrite the output files without asking, as if l_confirm=no .
• option unique makes the program ignore hits with sequences 100% identical to the query set (if one sequence is a fragment of another, they are is still considered 100% identical).
• option protein or nucleotide limits the search to database sequences only of this type. It is important for PDB sequence database since it contains both protein and nucleic acid sequences.
• option type automatically selects protein or nucleotide based on the query sequence type, but only if you search with a single sequence.

• alignMinCoverage (default 0.5) a threshold for the ratio of the aligned residues to the shorter sequence length.
• alignOldStatWeight (default 1.) a parameter influencing the statistical evaluation of sequence comparison. To use run-time statistics use alignOldStatWeight=0.
• Up to mnSolutions hits will be retained in the final table of hits.
• The parallel version of the program will use nProc CPUs (but not more than is available in your computer). The expected time is inversely proportional to the number of CPUs.
• maxMemory is a real ICM-shell-variable defining the size of the database buffer memory in Mb used by the command. If this size is smaller than the database, the sequences will be loaded in chunks.

 
#>T SR                                                 
#> NA1 NA2            MI     MX   LMIN    LN     H      ID      SC      pP   DE  
1hiv_a POL_HV1H2      57    155     99  0.665  0.099  100.0  103.69   30.00 "POL PROT.." 
1hiv_a POL_HV1BR      69    167     99  0.664  0.098   99.0  103.62   30.00 "POL PROT.. 
<i>... lines skipped ...</i> 
1hiv_a POL_MLVAV       9    102     99  0.648  0.078   27.3   23.41    5.31 "PROTEASE.." 
1hiv_a VPRT_MPMV     172    272     99  0.799  0.290   29.3   21.95    4.82 "PROTEASE.." 
1hiv_a VPRT_SRV1     172    269     99  0.799  0.290   27.3   21.65    4.72 "PROTEASE.." 
1hiv_a GPDA_RABIT     33    145     99  0.785  0.264   28.3   20.98    4.50 "GLYCEROL3P" 

• NA1 - the query sequence (a single command can search several query sequences)
• NA2 - the name of the database sequence
• MI : MX - the matching fragment boundaries in the database sequence
• QMI : QMX - the matching fragment boundaries in the query sequence
• LMIN - the shortest sequence length in a pair (query, database sequence)
• LN - log-correction factor (not used in pP but you may want to use it to resort the table).
• H - the fraction of the database sequence covered by the alignment with the query. If you search against a database of domains this number should be close to 1 (e.g. the hit is less significant if your query is only a part of a domain). It can be taken into account by multiplying pP by this number.
• ID - percent sequence identity (number of identical residue pairs in the alignment divided by LMIN)
• SC - normalized alignment score which is used to calculated the Probability. The score depends on the residue substitution matrix and gap penalties. (see the Score function).
• pP = -log₁₀ ( Probability )
• DE - the database sequence definition

 
 s_searchDB = s_icmhome + "/data/blast/pdbseq"
 read sequence "GTPA_HUMAN.swi"  
 find database s_searchDB output="gtpa1"  
 find database pattern="C?[DN]?\{4\}[FY]?C?C" s_searchDB margin = 5 
 
 unknown1=Sequence("TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN") 
 find database exact unknown1 s_searchDB margin=1 

find database fast [ = i_speed] sequence s_dbFile [output=s_file] [name=s_tabName]

very fast dictionary-based sequence search algorithm. Requires a blast-formated database file. Options:

• fast= i_speed # a number from 1 (slow, rigorous) to 100 (fast and only almost identical sequences).
• output= s_file # saves the output to a file.

Example:

read sequence swiss web "1433B_HUMAN" # read one sequence 
find database fast=90 1433B_HUMAN     # search pdbseq database (the default)

See also: write index sequence command that creates BLAST files from a FASTA file.

find molecule: chemical substructure search

[ find-molecule-sstructure ]

• prepare the target strings with the Smiles( a_//![hdt]* ) function (exclude hydrogen, deuterium and tritium)
• search the source string made without hydrogens

• i_out - contains the number of hits
• I_out - contains the integer array of the hit numbers

WARNING: This is obsolete way of chemical substructure searching. Use: find table Index chemical other chemical functions

find molecule reverse ms_1 s_smile

WARNING: This is obsolete way of chemical substructure searching. Use find chemical instead.
: find molecule sstructure [ all ] [ tether ]

find maximal common substructure in selected atoms of the two molecules. Without the all option, one largest pair of matching fragments is identified.

Options:

• all : finds multiple matching fragments. Takes fragments with number of atoms >= minMCSFragmentSize (3 by default )
• tether : tethers the matching as_molIcmObj2 atoms the equivalent atoms of as_molObj1 .

The tether option is useful since once the tethers are established, you can superimpose a_//T according to these tethers, or optimize the molecule with tethers, e.g.

build smiles "C(=CC=C(C1)CN(CCNC2)C2)C=1"
build smiles "C(=CC=C(C1)N(CCNC2)C2)C=1"
ds a_*.
find molecule sstructure all tether a_1. a_2.
superimpose a_      # uses tethers to superimpose a_ on a_1.

find molecule [ tether ] as_subFragmentQuery as_IcmTargetContainingQueryFragment
You can also use the alternative set of arguments and use molecular selections instead of the smiles strings. The atoms of as_IcmTargetContainingQueryFragment aligned to each sequential atom of the query molecule will be stored in the S_out array. The atom selection of the target will also be returned in the as_out selection.
The tether option: After the equivalent sets of atoms in two molecules are identified, tethers can imposed pulling atoms of as_IcmMolContainingQueryFragment to the equivalent atoms of passive atoms as_subFragmentQuery . The matching atoms of the second selection as_IcmMolContainingQueryFragment which are pulled by tethers to the as_subFragmentQuery template positions can be superimposed with the minimize "tz" v_positionalVariables command.
Important: unselect the hydrogens to speed up the matching procedure, e.g.

  find molecule a_1.//!h* a_2.//!h*

An example:

 
 build string name="a" "se nter his cooh"   # query template 
 build string name="b" "se nter his trp cooh" # target 
 find molecule a_a./his/cg,nd1,ce1,ne2,cd2,cb,ca,n a_b. tether 
 display as_out xstick # the tethered atoms of the target 
 display a_*. 
 minimize "tz" a_b.//?vt* 
 show Rmsd( a_b.//* )  # will show the RMSD of the equivalent atoms 

find chemical ms_sel s_smarts [all]

Searches using smarts pattern s_smarts in ms_sel. The result (matched atoms) will be stored in as_out With all option it'll find all possible matchings.

Example:

 build smiles "CC1=NN=C(NS(C(C=CC(N)=C2)=C2)(=O)=O)S1" name="sulfamethizole"
 display wire
 find chemical a_ "a" all  # finds all aromatic atoms
 display xstick as_out
 find chemical a_ "[$(N~[a;r6])]" all  # finds nitrogen bonded to 6-member aromatic ring
 display cpk as_out

See also: find molecule sstructure SMILES/SMARTS description

find pdb: fragment search

find pdb rs_fragment os_objectWhereToSearch s_3D_align_mask [ s_sequencePattern [ s_SecStructPattern ] ] [ r_RMSD_tolerance]
Find a fragment (e.g. a loop) with certain geometry, sequence and/or secondary structure. Arguments:

• rs_fragment: the search fragment template
• os_objectWhereToSearch: the other object.
• s_3D_align_mask: marks the residues to be used in the 3D superposition and comparison in terms of r_RMSD_tolerance (see below). The number of 'x's (or 'ON' bits) in the mask must be equal to the query fragment length (it may be discontinuous), while the total mask length should be equal to the found fragment length. For example, if you search for an 11-residue loop with the same geometry of 3-residue ends, but any geometry of the middle part your mask must be "xxx-----xxx". If you want to match geometry of the middle part you would invert the mask: "---xxxxx---", etc.
• s_sequencePattern: Use "*" for any sequence. Otherwise you may use regular expressions, for example: "?A[!P]???$".
• s_SecStructPattern: Use "*" for any secondary structure pattern. Otherwise, specify a regular expression, for example "?HHH___EE[!_]".
• r_RMSD_tolerance: RMSD threshold to accept a fragment as a solution. To avoid time-consuming optimal 3D superposition during the search, distance Rmsd (i.e. root-mean-square deviation between two Ca-atom distance matrices of the compared fragments) is used as a measure of spatial similarity on the preliminary stage of each comparison. However, in the resulting list of hits, collected in SearchSummary string array the optimal 3D superposition coordinate Rmsd is presented. Therefore, RMSDs in the output list may exceed the specified threshold.

 
 read pdb "1crn" 
 read object s_icmhome +  "complex"         # object in which to search 
 find pdb a_1./16:18,20:22 a_2. "xxx----xxx" "V[LIVM]?????G??" "*" 2.5
 print s_out

 
 read sequence "zincFing.seq" 
 find prosite 1znf_m            
 show SITES 

• ^ sequence beginning
• $ sequence ending
• ? one character
• * any number of any characters
• [ACD] alternatives
• [!ACD] all but the specified residues
• char \{ i_min, i_max \} : repetition. E.g. ?\{5,8\} from 5 to 8 of any character.

• number - just report the number of hits instead of reporting each match
• mute - suppress terminal output (used in scripts)
• i_mnHits - (default mnSolutions )
• os_objectWhereToSearch - the target molecular object.
• seq_Name - the target sequence. By default, the search is performed among all currently loaded sequences.
• seqNamePattern - the target sequence name pattern to search through many sequences loaded to the shell.

• s_out - text output of all matches
• i_out - the number of hits
• r_out - the ratio to the random expectation (it r_out>1. it means that the number of hits is larger than the random expectation).

 
 read sequence s_pdbDir + "/derived_data/pdb_seqres.txt"  # all pdb-sequences  
 find pattern "[AG]????GK[ST]"   # search for ATP/GTP-binding sites  
 searchPatternPdb "^[LIVAFM]?\{115,128\}[!P]A$"    
     # ^ : seq.start; ?\{115,128\} from 115 to 128 of any res.; $ : seq.end  

find molcart [sstructure|similarity|exact] table=s_molcartTable [ s_smarts|S_smarts|chemarray ] [r_distCutOff] [only] [stereo] [name=s_resultName] [query=s_SQL_condition] [output=s_molcartTable] [number=i_maxHits] [exclude=s_smarts|S_smarts] [append|delete] [ connection_options ]

Performes chemical search in Molcart database. Connection may be specified by connection_options

Supported search modes are:

• exact : exact match
• sstructure : substructure
• similarity : find similar compounds with distance cutoff r_threshold (between 0 and 1)

Other options:

• The output option allows to save search results in another database table s_molcartTable. It is possible to specify a table in another molcart connection by using "connectionID;database.table" format.
• With append option, search results will be appended to the output table, if it exists.
• With delete option, the specified output table will be overwritten if it already exists.

Examples :

  find molcart sstructure table="screenpub.AllVendors" "c1ccccc1" number=1000 name="myHits"  # finds by substruture
  find molcart sstructure table="screenpub.AllVendors" "c1ccccc1" number=1000 filter="=4" name="myHits"  # finds by substruture (contains 4 benzene rings)
  find molcart exact table="screenpub.AllVendors" t.mol  # finds exact matches. chemical array pattern
  find molcart similarity 0.2 table="screenpub.AllVendors" "CC1=CN(C(NC1=O)=O)[C@H]1C[C@@H]([C@H](CO)O1)O" # find by similarity with distance <= 0.2

See also: Index chemical Nof Find find table

find table : chemical search in ICM table

find table {T_table|filename=<s_file} {sstructure [group]|similarity|exact} [ s_smarts|S_smarts|chemarray ] [r_distCutOff] [only] [stereo] [query=s_ICM_condition] [name=s_resultName|select] [index=I_index]] [append]

Performs chemical and text search in the local table.

Arguments:

• T_table : input table.
• Alternatively an SDF or CSV s_file may be specified.
• s_smarts or S_smarts chemarray : input pattern
• search type: sstructure similarity exact
• r_distCutOff distance cutoff for similarity search
• With stereo option chirality will be taken into account in substructure and similarity searches.
• group option toggles the special search mode when all atoms in the pattern except attachment points are treated "as drawn" (not other attachments are allowed)
• With only option only number of hits will be returned.
• With select option matched rows in the original table will be selected (not result table will be created)
• name=s_resultName result table name (ignored with select option)
• query=s_ICM_condition extra condition. Using this argument you can specify an extra logical condition for the query. Column names, string constants and numnbers can be used: For example : MolWeight<400
• With append option, search results are appended to the result table

Examples :

  group table t Chemical({ "CC(=O)Oc1ccccc1C(O)=O", "CC(Nc1ccc(cc1)O)=O" } ) "mol"
  add column t Mass(t.mol) name="MW"
  find table t query = "MW<160" select  # select rows with molecular weight < 160
  
  group table t2 Chemical({ "CC(=O)Oc1ccccc1C(O)=O", "CCCc1c2c(C(NC(c3cc(ccc3OCC)S(N3CCN(C)CC3)(=O)=O)=N2)=O)n(C)n1" } ) "mol"

  # compare chemical tables
  find table exact t  t2.mol select   # select rows in t 
  find table exact t2 t.mol  select   # select rows in t2

  find table similarity t  t2.mol select 0.5   
  find table similarity t2 t.mol  select 0.5  

  # Not enough? Let's increase distance cutoff

  find table similarity t  t2.mol select 0.8   
  find table similarity t2 t.mol  select 0.8  

  # this command can also be used to select arbitrary rows in a table
  find table t2 select index = {1 3 5}
  Index( t2 selection )
  

See also: Index chemical Find find molcart SMILES/SMARTS other chemical functions

find pharmacophore : pharmacophore search in ICM table

find pharmacophore as_pharmQuery chemarray3D [all]

Performs a pharmacophore search in chemarray3D using as_pharmQuery.

Example:

read binary s_icmhome + "example_ph4.icb"
find pharmacophore  a_pharma. t_3D.mol

all option allows to score all possible mapping for each conformation

See also: Rmsd superimpose makePharma

fix

fix vs_
fix (exclude from the free variable list) specified variables (such as bond lengths, angles and phases or torsions) in an ICM-object. This operation can be applied to the current object only (use set object os_object first). See also: unfix .
Examples:

 
 set v_//omg 180.                # set all omega torsions to the ideal value  
 fix v_//omg                     # fix all omega torsions  
 
 fix v_/8:16,32:40/phi,PSI,omg*  # fix the backbone in two fragments 

 
 icm _multiProc  # from the unix shell or 
 unix icm _multiProc  # from the interactive ICM-shell 

 
 read libraries 
 macro bigDatabaseJob i_nChunks i_Chunk s_outFile  # definition 
  ... 
 endmacro 
 
 read sequence "hot" 
 fork 4   
            # spawn 4 extra processes, total 5 
 bigDatabaseJob 5  iProc  "out"+iProc  
            # work on section iProc, 
            # save results to files out1 out2 .. 
 wait       # also quits all extra processes 
 unix cat out1 out2 out3 out4 out5 >! out.tab 
 read table "out.tab" 
 .... 
 quit 

 
 fprintf        "a.txt" "%s\n"      "Day Temparature" 
 fprintf append "a.txt" "%s %.2f\n" "Monday", 22.4  
 fprintf append "a.txt" "%s %.2f\n" "Tuesday", 27.334  

 
macro read_alignment s_file 
  global read alignment s_file 
endmacro 

[ group sequence | Group sequence unique | group table | Group column ]

• longer sequence is better that shorter
• if the names contain the X-ray resolution 2 digit suffixes (like a19 and 9lyz24, for resolutions 1.9 and 2.4 respectively), higher resolution is better (1.9 is better than 2.4). Note Resolution suffixes are added by the read pdb sequence resolution command
• higher number in a pdb-file name is preferable, i.e. 9lyz is better than 3lyz. (I would not die for this principle, though).
• identical chains have alphabetical preferences (e.g. 9lyz_a is better than 9lyz_b).

 
 read sequences s_icmhome+"seqs.seq" # load sequences   
 group sequence aaa                  # group ALL the sequences into aaa 
 group sequence seq3 seq1 seq2 aaa   # explicit version of the previous line  
 align aaa                           # multiple alignment  
 
 read sequences s_icmhome+"azurins.msf" # some of sequences are very close  
                                     # but not identical   
 group sequence myAzur unique 0.15   # 0.15 is a Dayhoff-corrected minimum  
                                     # intersequence distance threshold  
 group sequence myAzur unique 26     # all sequence pairs differ in  
                                     # more than 26 positions  
 group sequence myAzur unique delete # duplicates will be removed 

• it can cluster/unique millions of sequences very quickly (your computer just needs enough memory).
• larger sequences incorporate the matching smaller ones.
• merged or absorbed sequence names are added to the description of their master unless nosort is specified
• merging (option "overlap") protein sequences requires sticky C-terminus letter 'X'
• the algorithm is based on a dictionary approach and allows to have mismatches
• matching rules:
  • for proteins: any letter matches 'X', B=(D or N) and Z=(E or Q)
  • for nucleic acids: any letter matches 'N'
  • if possible, 'X','N','B','Z' are replaced by a more specific letter from the matched sequence

• delete - the non-unique sequences are deleted not only from the group but also from the shell
• nosort - do not merge descriptions of the merged sequences
• unique= "simple" - the fastest mode. It will eliminate only the exact duplicates.
• unique= "nt" means that DNA or RNA sequences are compared (the program assumes protein sequences by default and a corresponding i_wordLen of six). This implies the alphabet of A,C,G,T (or U) and the word length should therefore be increased. The default nucleic acid sequence word length of 13 allows to fit the entire dictionary into the memory of 256 Mbyte. If your computer has less memory, reduce the i_wordLen to a smaller value.
• unique="junk" this option tells the program to remove sequences that do not contain any meaningful sequence. This means that they are mostly composed of 'X's or 'N's and the intermittent sequence is shorter than i_wordLen. This option is almost always useful.
• unique="stripX" this option tells the program to strip X (or N for nucleotide) character stretches from the beginning and from the end of the sequence. Those will be compressed into just one character. Useful if your sequences were dusted or repeat-masked.
• unique="noX" this option tells the program to skip the sequence quality enhancements (replacement of 'X','N','B','Z' by a more specific letter from the other very similar sequence).
• unique="complement" with this option the complementary nucleic acid sequences will also be considered and removed if redundant. This option can not be combined with the "overlap" option.
• unique="overlap[>numberOfRes]" Merge overlapping fragments in in addition of deleting the subfragments from the set. The number of overlaping nucleotides or amino acids can be redefined, e.g. unique ="overlap>25"
  • Two amino acid sequences are merged only if there is the overlap is greater than the threshold (12 amino acids by default) and the overlapping C-terminal residue is 'X'. An example of the allowed merge for protein sequences:

     
    s1     VTIKIGGQLKEALLDXGADDTVLEEMSLPGX------- 
    s2     ----------EALLDTGADDTVLZEMSLPGRWKPKMIG 
    result VTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIG 
    

    If for some reason your ESTs do not terminate with 'X's, they can be added by the following procedure:

     
     for i=1,Nof(sequence ) 
       sequence[i] = sequence[i] //Sequence("X") 
     endfor 
    

  • Two nucleic acid sequences are merged if the overlap is 30 by default. There are NO special requirements for an 'X' nucleotide flanking the sequences.
• i_wordLen (6 by default, 14 if the unique="nt" option is specified). The length of a word in the dictionary. The memory occupied by the dictionary depends exponentially on his length.
• i_dictDepth (10 by default) limits the number of sequence fragments referenced referenced from a single 'word'. This option prevents the dictionary from growing to much in memory (what the product of i_wordLen * i_dictDepth ) .
• i_nofMutations (zero by default) the maximal number of mutations/mismatches between sequences which are considered to be redundant.

• Trans( seq_ frame ) - to translate a DNA sequence
• align new # to align a cluster and generate the consensus
• Find( sequence , s_keyword ) # to find a retired sequence with the s_keyword in its title among the newly formed sequences
• show [color] ali_

WARNING: The append option of this function is obsolete. Use add column instead.

create a new table from individual arrays or append new columns or table header elements to an existing table. This example shows how an ICM table including both header elements and columns may look like:

 
group table t {1 2} "a" {"one","two"} "b" header "trash" "comment" 2001 "year" 
 Info> table  t  (2 headers, 2 arrays) has been created 
  Headers: t.comment t.year 
  Arrays : t.a t.b 
 
show t 
 #>s t.comment                   # TWO HEADER ELEMENTS 
 trash 
 #>i t.year 
  2001 
 #>T t 
 #>-a-----------b----------      # TABLE ITSELF 
    1           one 
    2           two 
show t.comment t.year 
 trash 
   2001 

• copy: make a copy of the original ICM-shell object and move it to the table.
• append: add specified ICM-shell objects to the table (default: overwrite).

See also: split, Table , add column (to append columns ) .
More examples:

 
 a=1   # integer a  
 b=2.  # real b  
 group table copy t header a "ii" b "rr"   
       # create table t with t.ii and t.rr header objects 
 show t 
 group table t header a "" b ""    
       # t with t.a and t.b header objects 
 show t 
 group table t {1 2 3} {2. 3. 4.}  
       # t with automatically named table 
       # arrays t.1 and t.2 
 show t 
 group table t {1 2 3} "a" {2. 3. 4.} "b"  
       # t with table arrays t.a and t.b 
 show t 
 split t # split the table into individual arrays 

Function	Description	Array Type
uniq	merge unique field values into v1,v2,v3	I,R,S
first	keep the first value in the grouped table	I,R,S
last	keep the last value in the grouped table	I,R,S
mean	find the mean value with the same key	I,R
min	find the minimal value with the same key	I,R,S
max	find the maximal value with the same key	I,R,S
rmsd	find the root-mean-square deviation of values with the same key	I,R
sum	find the sum of values with the same key	I,R

Example:

 
group table t {1 2 1 1 2} {1. 2. 3. 4. 5.} 
t 
 #>T t 
 #>-A-----------B---------- 
    1           1. 
    2           2. 
    1           3. 
    1           4. 
    2           5. 
 
group t.A 
t 
 #>T t 
 #>-A-----------B---------- 
    1           1.,3.,4. 
    2           2.,5. 
 
group table t {1 2 1 1 2} {1. 2. 3. 4. 5.} 
group t.A t.B "sum,C"  # sum t.B values and call the column C 
#>T t 
#>-A-----------C---------- 
   1           8. 
   2           7. 

There are two special rules "refmin" and "refmax" which can be applied in conjunction with "min" and "max" and allow to take rows corresponding to minmum or maximum values in the group.

Note that specifying all option instead of column name will apply operation for all the rest of columns.

Examples:

group table t {1 1 2 2} {2 1 3 4} {"a" "b" "c" "d"} {"a" "b" "c" "d"}
group t.A t.B "min,B"  all "refmin,C"  name="t1"
group t.A t.B "max,B"  all "refmax,C"  name="t2"

 
% icmgl 
 gui simple 

 
icm -g # or  
icm -g mymenus.gui 
icm -G mymenus.gui  # keep the original terminal window 

 
XTermFont *-fixed-medium-*-*-*-24-* 

 
 undisplay window  

See also: gui programming

help

[ Help browser | help | help commands | help functions ]

help command|function|icmVariable|s_icmHelpAncorName

help "I:anchorName"

open the specified section in the ICM Language Reference Manual

help "G:anchorName"

open the specified section in the ICM Program Guide

help s_htmlFileName # the file name must be followed by the pound sign

opens a single html file in the built-in ICM html browser. This file may contain sections of icm script in the following format:

<!--icmscript name="action1"
read pdb "1crn"
display a_*.
-->
...
<a name="action1" href="#action1">click here to execute icm script</a>

help read pdb  # opens the read-pdb section
help "G:learning"
help "I:montecarlo"
help "myfile.html#"

help command|function|icmVariable|icmHelpAncorName

help

help [ input= s_fileName ] [ word1 word2 ... ]
get full help in either text or html form, redirect it to the specified file, if the input option is specified. Do not use plural forms of the nouns. Examples:

 
 help Random 
 help read sequence 

 
 help                     # type  /stereo, and then letter n or Bar 
 
 help help                # how to get help  
 
 help commands            # list syntax of all commands  
 
 help commands  "rea*"    # list syntax of all read commands  
 
 help functions           # list syntax of all functions  
 
 help functions Matrix    # list syntax of the Matrix family of functions  
 
 help                     # start the browser to use its own search means  
 help montecarlo          # just the command name  
 help real constant 
 
 help read pdb 
 
 help Split 

For example:

 
 history 20              # show last 20 lines  
 history unique 

[ Info molcart ]

info auto write

Shows information about when autosaving was performed in the current session.

Database additional statistics

info molcart [ connection_options ]

Prints additional information about the Molcart connection. Connection may be specified by connection_options

See also: molcart

keep

keep ICM-shell-variable-name1 .. [global]
retain specified ICM_shell variables or their classes (e.g. real, rarray etc.). This command is used in macros to avoid automatic deletion of all the local ICM-shell variables.
Also note that four classes of standard ICM-shell variables, reals, integers, logicals, and preferences, are automatically restored to their initial values by default. You can use the keep command to retain their new values.

Examples:

 
 macro rdseq s_pdbName  # extract sequence from a pdb-file 
   read pdb sequence s_pdbName 
   rz = Resolution(s_pdbName,pdb) 
   mncalls = 10         # the existing standard shell variable 
   keep rz, sequence    # retain all the sequences and rz 
   keep mncalls         # retain its new value 
 endmacro   

Note that by default values will be kept only for the one level higher. With global option changes are propogated through the all nested levels to the global namespace.

Example :

s_a = "global"
s_b = "global"
macro m1
  m2
  print "m2: ", "s_a =", s_a, "s_b=" s_b
endmacro

macro m2
  s_a = "m2"
  s_b = "m2"
  keep s_a   # will be kept only for m1
  keep s_b global  # will be kept globally
endmacro

m1
print "global: ", "s_a =", s_a, "s_b=" s_b

join [left|right] T1.co1 T2.col2 [ name= s_newTableName ] [ column=S_outputColumns ] [stereo off]

Unites some or all data of the two tables into another table. If the s_newTableName coincides with the one of the tables, the new table will replace it. The default output table name is T_join .

The main two arguments are two columns T1.col1 and T2.col2 with matching values. You can use chemical structure column to join by exact structure match. stereo off option can be added to ignore chirality.

The column= argument contains the list of column names to be retained in the output table.

Columns in the new output tables.The columns for the output table can be listed as the column= By default action is to include all columns from both tables. The columns by which the tables are joined will turn into one, therefore the total number of columns by default will be N1+N2-1.

Column names of in the joined table.The column takes are preserved unless they collide (i.e. T1.B and T2.B are both present). The the latter case the first column retains its name while the column from the second table will be named T2name.colName , (e.g. T_join.B , T_join.T2_B ).

Types of the join commandThere are three types of the join command:

• inner join - the default mode, no keyword needs to be specified. The inner join returns all rows from both tables where there is a match in the order of the T1.col1 column. If there are rows in T1.col1 that do not have matches in T2.col2, those rows will not be included in the output column. This table can easily be empty, if the values do not overlap. The number of rows of the output table is less or equal to the number of rows in the first table. Example:

  
  group table t1 {1 2 3} "A"  # 1 has no match in t2
  group table t2 {"a" "b" "c"} "A" {2 3 4} "B"
  show t1,t2
   #>T t1
   #>-A----------
      1
      2
      3
   #>T t2
   #>-A-----------B----------
      a           2
      b           3
      c           4
  
  join t1.A t2.B name="t3"
  t3
   #>-A-----------t2_A-------
      2           a
      3           b
  

• leftThe left join returns all the rows from the first table, extended with the matching rows from the second table. For T1.col rows there with no matches in the second table, empty fields will be added. The number and order of rows of the output table is equal to the number of rows in the first table. Example:

  
   group table t1 {1 2 3} "A"  # 1 has no match in t2
   group table t2 {"a" "b" "c"} "A" {2 3 4} "B"
   join left t1.A t2.B
   T_join
   #>T T_join
   #>-A-----------t2_A-------
      1           ""
      2           a
      3           b
  

• rightthe right join returns all the rows from the second table, and appends fiels from the first table if a match is found. It is identical to the left join but with two arguments swapped ( join left t1.A t2.B is the same as join right t2.B t1.A ). Example:

  
   group table t1 {1 2 3} "A"  # 1 has no match in t2
   group table t2 {"a" "b" "c"} "A" {2 3 4} "B"
   join t1.A t2.B right name="ttt"
   ttt
   #>T ttt
   #>-A-----------B----------
      a           2
      b           3
      c           4
  

• localthe local join returns all the rows from the first table. Values in the matching (by name) columns will be overwritten with values from the second table for matched rows. Example:

  
  add column t1 {1 2 3} {1 2 3}
  add column t2 { 2 3} {4 5}
  join t1.A t2.A local name="t1"
  

See also the add table ( command for appending a table with identical column structure ) add column or add column function ( adding new columns )

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learn from a training data set and create a predictive model

[ Learn atom ]

Options:

type="pls"|"pcr"

- the training method

kernel="dot"|"polynomial [iOrder C0]"|"radial [exp]"|"tanimoto"|"sigmoid [K C]"

name= s_outputModelName

column= S_columnNames

- an array of column names

all

- forces to use all numerical columns in addition to the chemical column

test [= nCross|I_excludedTestRows] # cross-validation group number or test rows

center # enforce the constant @@{w,,0} (see below) to be **zero .