Copyright © 2005, Molsoft LLC
Aug 8 2008
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[ Build faq | Convert pdb | Regularization procedure | Molecule create | Molecular modifications | Objects merge | Merge2 | Xyz morphing | Stereo reconstruction ]
How to build new object from a sequence |
The easiest way to build an object with one of several peptides is to use the build string command. There you can use a one letter code (upper case characters) or three-letter code and separate sequences of different chains by a semicolon. Examples:
build string "AAAAA" # penta-alanine build string "ASFHGD;EQWR" # two chainsTo create a DNA duplex or a compound, use GUI.
For a more flexible building procedure, follow the following steps:
- Create the ICM sequence file either manually or using IcmSequence function, e.g.
write IcmSequence( "FAASVRES", "nh3+", "coo-") "file.se" read sequence "memb.seq" # creates the ICM sequence memb write IcmSequence( memb , "nh3+", "coo-") "myseq.se" build "myseq"
You can also build sequence directly without creating a file with the build string . See the build command and IcmSequence( ) function. - Change the default conformation using the available information. Possibilities:
Examples:
build string "se nh3+ ala his leu trp coo-" set v_/3/xi1 -60. minimize
How to quickly convert a pdb file into an ICM-object |
Sometimes it is necessary to have a PDB file in the form of an ICM molecular object. For example, it's a convenient way to list and/or to change a torsion angle (or a series of them). All what you need is to use convert command. One more ICM-format object will be created (use show object command to see the list of currently loaded molecular objects). The above method is good only for a limited set of tasks mostly related to structure analysis. If you want to perform further conformational sampling by energy optimization it is better to regularize the pdb-object (see the next section)
We recommend to use the convertObject macro which optimizes hydrogens and can do some necessary cleanup.
See also strip
How to prepare a PDB structure for energy calculations (regularization) |
Regularization is a sophisticated multi-step procedure. It consists of the following six steps.
- Preparation of a file with the amino acid sequence.
- Creating full-atom ICM-model (geometrical approximation).
- Rotational positioning of methyl groups.
- Iterative optimization of geometry and energy of the whole structure.
- Adjustment of polar hydrogen positions.
- Free minimization to check the consistency of the resulting structure.
How to create a new molecule or a residue for the ICM residue library |
Let us assume that your input is a pdb file with a new small organic molecule and you want to create a proper ICM object from this molecule. What is currently missing in the description may be the following:
- proper chemical bond types (single, double, triple, aromatic). To see them press Ctrl-W to switch to wireStyle="chemistry".
- hydrogen atoms (you need proper bond types to add hydrogens)
- proper atom types
- partial atomic charges
- directed graph (ICM-tree) imposed on all the atoms. This graph defines torsion angles and will be built by the write library command. In an ICM object the graph can be displayed if wireStyle="tree".
- read pdb "ligand" # molecule has no hydrogens display
- set bond type 1 a_//* # initialize all bond types by 1, the default is 0 # 0 type means that the convert command will try to guess the type
- set bond type 2 a_//o2 a_//p1 # type 'set bond type 2' and Ctrl-rightClick two atoms # set all other non single bonds: 1-single, 2-double, 3-triple, 4 aromatic.
- set bond type 4 a_//c1,c2,c3,c4,c5,c6 # an example of setting aromatic type for a ring
- build hydrogen # use 'delete hydrogen as_' if things go wrong
- set type mmff
- set charge mmff write library command to save the residue entry file or append it to the icm.res or create you own library file.
How to modify an ICM-object: some standard modifications. |
[ methylation | hydroxylation | glycosylation | sulfation | amidation | phosphorylation | ssbond-formation | peptide-bond ]
Methylation, hydroxylation, glycosylation, sulfation, amidation, phosphorylation, disulfide bond formation, peptide cyclization/bond,ICM allows to perform most of the common chemical modifications of peptides and other biological molecules. It is easy to build a linear chain of amino acids and add N- and C- termini. D-amino acids can be introduced by adding capital D in front of the residue name (i.e. Dala). To make further modifications we will use the modify and the make [disulfide | peptide] bond commands. Let us consider the main categories, using the nh3-DCSTVYHCK-coo peptide as an example. Start you session with
build string "se nh3+ asp cys ser thr val tyr his cys lys gly coo-"Now, if you like to see the results of your operations, display the molecule and do the following:
- type modify in the command window;
- Ctrl-RightClick on the atom of interest (the selection will appear in the command window);
- and, finally, enter the quoted chemical group name and press Enter.
-
Methylation:
...-NH-... + CH3 ->...-N-CH3 + H
modify a_/val/hn "ch3"
-
Hydroxylation:
...R-CH2... + OH ->...R-CHOH... + H
where R belongs to side-chain of Lys or Pro.
Examples:
# 5-hydroxylysine (Hyl) in collagen modify a_/lys/hd2 "oh" # 4-hydroxyproline (Hyp) in collagen modify a_/pro/hg2 "oh" -
Glycosylation:
1. O-glycosylation:
...-R-OH + O-CH- Carb ->...-R-O-CH- Carb + OH
where R is a side-chain radical of Ser or Thr and Carb
is an O-capped carbohydrate. Groups available for O-glycosylation are
"acgl", "xyl", "agal", "bgal". You can further modify these groups.
Examples:
modify a_/ser/og "acgl" # beta-D-N-acetylglucosaminide modify a_/thr/og1 "xyl" # xylose
2. N-glycosylation: ...-R-NH2 + O-CH- Carb ->...-R-NH-CH- Carb + OH where R is a side-chain radical of Asn. Carb is an O-capped carbohydrate (see O-glycosylation above). The following example illustrates an alternative way of modification when a part of the attached group is disregarded.# It is assumed that the modified object (a_1.) is already built. # Now build the second object including only one aclg residues. build string "se acgl" "modgroup" display a_ red set object a_1. modify a_/asn/hd21 a_2.1/1/c1 # o1 atom of the acgl is disregarded, and # asn's Nd and acgl's c1 is directly connected. delete a_2. # Remove obsolete second objectIf glycosylation follows hydroxylation, you explicitly do the same by N-glycosylation:modify a_/lys/hd2 "oh" modify a_/lys/o_a "bgal" # o_a is the new unique name for the oxygen
Alternatively (and preferably) replace hydrogen directly:modify a_/lys/hd2 "bgal"
-
Sulfation:
...-R-OH + SO4 ->...-R-O-SO3 + OH
where R belongs to Tyr.
modify a_/tyr/oh "sul" # tyrosine-O-sulfate in fibrinogen
- Amidation of the C-terminal glycine: Build the peptide with the last gly replaced by the conh C-terminal residue. Tether it to the previous object and minimize tethers.
-
Phosphorylation:
...-R-OH + O-PO2-OH ->...-R-O-PO2-OH + OH
where R belongs to Ser, Thr, Tyr
or
...-R-H + O-PO2-OH ->...-R-O-PO2-OH + H
where R belongs to Lys, His
or
...-R-O + O-PO2-OH ->...-R-O-PO2-OH + O
where R belongs to Asp.
modify a_/ser/og "pho" # skip if you have already modified this residue modify a_/thr/og1 "pho" modify a_/tyr/oh "pho" modify a_/lys/hz2 "pho" modify a_/his/hd1 "pho" modify a_/asp/od2 "pho"
-
Disulfide bond formation:
...(cys)-S-H + H-S-(cys)... ->...(cyss)-S-S-(cyss)... + H2
(note that names of the residues are changed upon bond formation (see
disulfide bond
).
#ds extended ICM model of the sequence display # set only one SS-bond, disregard all previous make disulfide bond a_/3 a_/9 only # MC search for plausible conformations montecarlo -
Peptide cyclization and peptide bond:
...COO + NH3... ->...-CO-NH-... + H2O
build string "se nh3+ gly gly gly gly his coo-" display make peptide bond a_/nh3*/n a_/his/c # form a cyclic peptide display drestraint minimize "ss" minimize "vw,14,hb,el,to,ss"
The following example shows how to build a cyclic peptide cyclosporin A:
# read pdb "1csa" # make bond a_1csa.m/1/n a_1csa.m/11/c # write library "cs" a_/1 # display grey build string "se thr thr gly leu val leu ala Dala leu leu val" modify a_/2/og1 a_/2/hb modify a_/3/hn "ch3" modify a_/4/hn "ch3" modify a_/6/hn "ch3" modify a_/9/hn "ch3" modify a_/10/hn "ch3" modify a_/11/hn "ch3" rename a_/1 "bmt" # actually, the residue BMT is more complex rename a_/2 "aba" rename a_/3 "sar" rename a_/4 "mle" rename a_/6 "mle" rename a_/9 "mle" rename a_/10 "mle" rename a_/11 "mva" display make peptide bond a_/11/c a_/1/n minimize "vw,14,to,hb,el,ss" montecarlo "vw,14,to,hb,el,ss"
How to merge two ICM-objects |
(the move command). It may be necessary to merge two or several ICM-objects or molecules to one, For example, if you are dealing with a docking problem and have prepared two molecular objects separately. The ICM command move allows you to do that. Technically, it rearranges virtual connections in the ICM molecular tree responsible for the description of the molecules in one ICM-object or in several ones.
read object "complex" # load a two-molecule ICM-object
display virtual a_//!h* # display molecules with virtual bonds
color molecule
show object # one ICM-object loaded
read object "crn" # load one more ICM-object
display virtual
color a_2. magenta
show object # two ICM-objects loaded
move a_2.* a_1. # merge two ICM-objects to one
# with virtuals connected to the origin
show object # now two loaded ICM-objects becomes one
connect a_1.3 # you can move newly incorporated molecule
# w/respect to the original complex.
# do not forget to press ESC key in the
# graphics window to complete the command
# and / or you can save the new
# three-molecule object to a new file
write object "super_complex"
(See connect to learn more about the command.)
If, on the contrary, you would like to have one or several molecules from an ICM-object as an independent ICM-object, you should simply delete unnecessary molecules and to save the remaining one(s) as a new ICM object, for example:
read obj "super_complex" # suppose you saved "supercomplex"
# from above example, then...
delete a_1.1 # all what you need is a_1.2 and a_1.3,
show molecule # right?
write object "remains_of_super"
# new ICM-object file "remains_of_super.ob"
# contains the 2nd and the 3rd molecules
How to make a hybrid model from several pdb files |
To swap parts between several pdb files, read all of them to icm, and rename the chain which are you going to graft into the template, so that the template and the graft have the same name. Sometimes the two structures need to be superimposed. So, what is important for 'graftability' is
- the graft has the same chain name (see rename )
- the graft has residue numbers consistent with the template (see align number )
- the graft has consistent coordinates (see superimpose )
read pdb "1crn"
read pdb "1cbn"
rename a_2.1 "m"
# or rename a_2.1 Name(a_1.1)[1] to do it automatically
superimpose a_1.1 a_2.1 align # see more specific
The second concern is residue numbers. They need to be unique. This can be performed with the align number command, e.g.
align number a_2.1/21:28 22 # renumber the loop starting from 22
Now you can write the pieces to a file and after you read it back the pieces will become one molecule.
write pdb a_1.1/1:20 "hyb" write pdb a_2.1/21:28 "hyb" append write pdb a_1.1/29:99 "hyb" append read pdb "hyb" # read the hybrid in cool a_ # display it
These operations are combined in the mergePdbmacro, e.g.
mergePdb a_2./20:25 a_1./300:308 # creates hybrid.pdb file
How to generate a series of intermediates between the two given structures |
The following procedure will solve the problem:
read pdb "bj1bb" # first structure
read pdb "bj2bb" # second structure
strt = Xyz(a_1.//*) # matrix (3, N_of_atoms) of the first ...
fnsh = Xyz(a_2.//*) # ... and of the second
display a_1. red # to see what is going on if you need it
display a_2. blue
nn = 300 # to generate 300 intermediate conformations
x = 1./nn
for i = 1, nn
set a_1.//* strt*(1.-x*i) + fnsh*x*i
write pdb a_1. "x"+i
# uncomment the above line if you need
# to save intermediates in x1.pdb, x2.pdb, etc.
endfor
quit
How to reconstruct a structure from a published stereo picture |
Follow these steps:
- Scan the picture and create arrays of arbitrarily scaled coordinates xLeft xRight and Y for the Ca atoms.
- When you have the coordinates in your ICM session call the makePdbFromStereo macro.
- mark the PDB-formatted lines and paste it after the read pdb unix cat command.
- inspect the results, possibly return to step 1 and correct the coordinates or use stereoAngle = -6.
- to build all-atom model, create sequence file and use the macro regul .
Example:
read column "xxy" # 3 numbers in each line + a header: #> xl xr y
makePdbFromStereo xl xr y 6.
read pdb unix cat
ATOM ....
ATOM ....
# Ctrl-D
display
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