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Reference Guide
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[ last-release ]

Version 3.5-1p Apr 16, 2008

• Extract Lingand also works with amino acid chains with < 20 residues
• Fixed bug with 'ND' values in join introduced in the 3.5-1o version.
• Fixed crash in export to Excel when table is in grid mode.
• Fixed crash in reading some SD files containing text entries
• Fixed bug in R-group decomposition.
• make hbond command does not generate an error when no hydrogen bonds were found. (only warning)
• truncation in assignment of a table with long column names might lead to a state with two or more columns with then same name. FIXED.
• read table csv treats empty values as 'ND' fields in numeric columns.
• smiles parser accepts r-groups with two digit number. Chemical( "[R10]" )
• symmetry group 'P42/n' added.
• Fixed progress bar indicator in homology modeling.
• added auto option for make molsar and split group commands
• Fixed bug in GUI dialogs created from Askg function. (return from 'o_' was not correct)
• Fixed problems with accessing tables as table[10] after tables were read from an .icb
• Preference for chain gap style: GRAPHICS.chainBreakStyle
• Preference for chain gap label style: GRAPHICS.chainBreakLabelDisplay
• Fixed bug in substructure search in find table command.
• join command preserves 'ND' values from source tables.
• write table csv preserves 'ND' values.
• fixed problem with residue number truncation in the workspace view.

Version 3.5-1o Mar 07, 2008

• TOOLS.sdfNewlineType preference is added. It controls newline style when writing SD/MOL files for compatibility with other applications.
• Fixed problem in calling APF superposition from the GUI Menu.
• '*' did not match aromatic atom in certain cases. Fixed.
• Fixed bug with negation '!' in SMARTS.
• Fixed crash in macroshape function (Linux only)
• Few adjustments in chemical similarity function
• Fixed bug in 3D editor (could not toggle chirality in certain cases)
• Fixed a few issues with resoring single/double bond order from aromatic systems with exocyclic double bond
• rename table checks if all columns can be renamed before actual renameing is done.
• Explicitly drawn hydrogens work as supposed in substructure search. ( find table Index Nof )
• Reactant dialog resizes properly.
• Functions to find element in array: Index( I i [all] ), Index( S s )
• New hydrogen bond mode "Show Intermolecular HBonds Only" can now be found in the hydrogen bond button's drop-down menu
• fixed crash in link variables command
• VISIBLE property had no effect on { o_option1 o_option2 } in GUI dialogs. Fixed
• : Tointeger( ), Integer( )
• new Split template: exact
• Fixed bug with default value interpretation in Toreal ( S_ S_ R_ )
• Fixed few problems with make reaction. Non-terminal R-groups were not processed properly in all cases.
• Added new templates for Name function Name( chemical | reaction | slide | model | tree )
• Fixed few problems in molecular editor :
  • added ability to connect two rings without creation of an extra bond between them (spiro compounds). Holding 'shift' button when placing a new ring will connect them directly through one common atom.
  • In default mode when an extra bond is created it did not rotate with a fragment when used press and move a mouse. Fixed.
• Fixed bug with setting table field properties from the form view.
• Fixed few problems with HEME ligand conversion.
• Added residue numbers for atom selection function
• join with left or right option insert ND (not-defined) values for rarray columns instead of zeros
• Improved composite keyword searching in documentation engine

Version 3.5-1n Jan 08, 2008

• Fixed problem with not preserving CIS/TRANS when editing 3D molecule in some cases.
• Fixed problem in refreshing table GUI when changing "displayStyle" header.
• Fixed problem with switching CIS/TRANS in 3D molecule editing
• Fixed problem with switching boat/chair in 3D molecule editing
• color by molecule preserves color for each molecule regardless of input selection.
• Skin can be displayed from any atoms in GUI.
• Added new preference which controls sequence offset display style. (GUI.sequenceOffsetStyle)
• Fixed few substructure search issues.
• Fixed bug when reading multiple protein objects from mol2 file.
• Fixed problem with Askg function. (Under certain circumstances it did not wait for the user input)
• Added possibility to add html links into txt_ tags. #txt_ (click here)
• Fixed bug in modify chemical find replace. With exact option formal charge modifications were not visible in GUI.
• Fixed bug in protein-protein docking.
• String ( ) skipped empty entries. Fixed.
• Fixed crash (or undefined behavior) when ICM script contains long (>512 characters) lines.
• Fixed crash in Index ( ) function
• Fixed problems in macroshape generation (bad triangles)
• Fixed bug in chemical substructure search with "stereo option" enabled.
• Alignment Tools Panel was shown on every command (even if it was closed). Fixed.
• color by alignment preserves color regardless of input selection.
• Fixed wrong nitrogen charging in some HEME ligands

Version 3.5-1m Oct 18, 2007

• Fixed crash when coping table rows in grid mode.
• Fixed bug in find molecule sstructure
• Fixed synchronization problem between 3D molecular table and 3D view. (Right click on 3D molecule in a table and choose "Edit" )
• New 'Ligand Pocket' menu item for molecule popup. Shows property colored surface.
• Fixed problem in Prot-Prot docking on Windows platform.
• Fixed bug in SMILES export. (it switched into SMARTS mode in some cases)
• Fixed 'buffer overflow' message in video recording.
• With -s or -w option ICM does not try to read preferences anymore (useful for CGI scripts)
• Fixed a number of issues with display/undisplay skin on several objects/molecules.
• Fixed problem with "display gui off"
• Fixed bug with changing GRAPHICS.NtoCRainbow
• Filter icon was not updated after filter add/clear. Fixed.
• Select rows by label appends to the selection.
• GUI.tableLabelSelection preference switches keyboard shortcut between selection and labeling.
• Fixed crash in alignment editor. (removing gap column after shading a box)
• Fixed problem with restoring current slide from slideshows loaded from file.
• Fixed problem with saving in slides hbonds for temporary objects from tables.

Version 3.5-1l Oct 7, 2007

• Fixed bug in display skin command with molecule option. (May lead to crash)
• Disable 'Save' menu item and toolbutton when project is read-only. Popup GUI dialog with an error message when trying to write in the readonly location.
• Fixed crash when calling chemical query dialog for 3D molecules with explicitly build hydrogens.
• Fixed rare crash when deleting object by right-clicking on tab and choosing 'Delete'.
• Fixed crash when reading CSV/TSV files with empty fields in rarray columns
• Fixed bug in expression evaluator for custom column coloring
• "Save/Save As" HTML called by right-clicking on tab works correctly if object is selected on the workspace.
• Fixed bug in reading mol2 containing empty lines.
• Fixed bug in table 3D browse mode when molecule consists of few fragments.

Version 3.5-1k Sep 26, 2007

• fixed reading of some "corrupted" ICB files created by 3.5-1h
• fixed rare crash with molecules covalently connected to two amino chains
• extended a library of unusual amino acids and nucleotides for read pdb command
• added blending effect for slide transitions.

Version 3.5-1j Sep 14, 2007

• fixed problems ("holes") in the molecular surface construction
• fixed bug in read mol2 command (wrong connectivity assignment if some atoms were skipped or do not have unique names)
• fixed matching bug in R-group decomposition
• fixed problem with opening/dragging file shortcuts on windows platform.
• fixed 'absurd in convert' problem for some pdb codes ("1bab")
• fixed bug chemical binary write (may cause crash when reading in some cases)

Version 3.5-1i Aug 17, 2007

• dynamic hbonds update corrected
• Fixed problem clipboard exchange with ISIS
• Automatically makes terminal visible on errors
• Copy Selection To Icm table validates input
• Hbond button update/refresh made more consistent with the current state of displayed hbonds in 'dynamic hbond' mode
• Recoloring skin by atom types fixed
• Deleting second atom selection variable fixed
• Added 'read string html "a.icb"' command to read all HTMLs from the file
• Fixed crash when deleting all rows in table.
• Cut/Copy/Paste column preserves format information (including row coloring)
• Switching between table view modes (TABLE-GRID-FORM) does not require focus (mouse click) anymore.
• Fixed random 'R-group dialog popup' when copying rows to other table.
• Fixed minimize/maximize problem in Chemical Search Space dialog. (minimize button removed)
• 'Merge Two Sets' dialog prompts for the result name.
• 'Unlock All' works with table names > 25 characters.
• Name(string html|command) functions to list all htmls/scripts in the shell

Version 3.5-1h Aug 10, 2007

• Some changes and renaming in Docking menu
• Fixed a crash in properties page of the docking hitlist.
• Lot of other small fixes and improvements
• a bug with passing same-name arguments in nested macros fixed

Version 3.5-1f Aug 1, 2007

BUG fixes:

• Fixed crash in read mol when provided name is too long.
• Fixed problem with empty menu in 'browser mode'

Version 3.5-1e June 24, 2007

BUG fixes:

• Fixed read mol2 command so it reads metal atoms
• Fixed crash in read table mol2 (read mol2 into a table)
• Fixed crash in Rmsd ( as1 as2 chemical )
• Fixed compatibility issues with older Molcart versions

Version 3.5-1d June 15, 2007

BUG fixes:

• Previously invisible single residue ribbon is now visible.
• Fixed few chirality issues in 3D conversion.
• Explicit hydrogens can be shown in 3D->2D mode.
• Fixed "Convert PDB" problem when there is no amino chains in the object
• Askg function supports title in the dialog declaration
• Fixed problem with "System Preferences" dialog: some editing actions were ignored
• Fixed problem with transitions between slides with locked and unlocked mesh/surface clipping planes
• Polar hydrogens show correctly for non-ICM objects
• find table supports 'exclude' option
• Copy molecular image from chemical table works for 3D chemicals
• New 3D labels now never override the existing ones
• read binary can read files without extension now

New features:

• command 'delete all' to delete all non-system objects in a shell.
• A family of new functions on oblique X-ray maps:
• Map(m_EDS ), Sign( map ), Abs ( map ), Index( m_EDS )
• Map( m_EDS cell ) => returns a map in crystallographic cell
• Index( m_EDS cell ) => returns 3 xr-cell index dimensions
• Index( m_EDS ) => returns various index cell dimensions
• make grob add # recontour map at new sigma level
• read mol2 for proteins with residues
• history jumps over repeating commands.
• sort object command to reorder objects in the list.
• GRAPHICS.occupancyDisplay preference is introduced. It allows to draw circles (and values) around atoms.
• set rs_ extended to allow repeats, e.g. set a_/A "H" means set all of them as "H", and "HE" is translated to "HEHEHE..."
• v_//L selection of standard free variables for newly build/converted objects. (L for ligands) Same as to v_//S for peptides
• GROB.contourSigmaIncrement parameter controlling the standard increment in contour levels
• column colors are preserved in a GRID table view.
• molecular objects are saved to disk much faster now
• in "drag atom" mode it drags atom exclusively. (SHIFT turns the old mode for ICM objects)
• movie production quality dialog

New in 3D labels (pair distances, hydrogen bonds, planar and dihedral angles):

• new objects: planar and dihedral angles (for 3 and 4 adjacent atoms respectively)
• double-click on 3D label in workspace panel selects atoms
• text labels of 3D label objects can be dragged to build nicer images
• improved hydrogen bond behavior: bonds jump to the proxy heavy atom when the hydrogen is undisplayed; current graphical selection is taken into account when rebuilding bond lists;
• labels are automatically displayed/undisplayed when the underlying atoms are shown/hidden
• 3D labels (except pair distances) are now completely stored into slides (previously objects were duplicated before being stored)

New commands/functions:

• delete variable
• delete plot
• Toreal( S S R ) : R
• select-3d-label

Version 3.5-1c June 09, 2007

BUG fixes:

• Fixed crash with empty chemicals in clustering and some table operations
• Fixed crash in PCA dialog
• Chemical( S_smiles ) does not break on error. Empty chemical are created instead.
• Interactive docking error when score is enabled. Fixed.

NEW features:

• temporary parameter re-definition for an ICM command . E.g.

  
  show energy "el" dielConst=8. electroMethod="Coulomb" l_info=no
  

  the parameters are automatically restored after the command.
• vwExpandDisplay parameter renamed to GRAPHICS.surfaceProbeRadius
• a new parameter, GRAPHICS.surfaceDotDensity, is introduced to control the dot density of displayed solvent accessible surface. It does not affect the energy/surface calculations.
• gpWeights to control the relative weights of the "gp" term in the energy+penalty function.
• APF superposition and alignment updated and number of issues are fixed.
• Graphical controls for dot surface density, dot size, probe radius
• Graphical control for clash style added.

Version 3.5-1b June 07, 2007

BUG fixes:

• fixed non-immediate displaying of 2D labels;
• fixed bug in stereo handling in smiles
• fixed bug when copied rows pastes as a column in a table
• annotate selection did not work on atom level. Fixed.
• R1,R2,.. matches a heavy atom only by default in reaction. [R1,H] will match hydrogen too
• grouping table by column:
  • fixed a crash on tables with bing number of columns
  • does not change original row/column order
  • redesigned a GUI dialog to handle large tables
• fixed crash with typing atom letter code over highlighted bond in workspace ligand view.
• popup menu on the tab sometimes does not activate tab under cursor
• allows editing "special values" for table cell. (<1,>1,ND)
• empty fields in SD files are not written by default for compatibility with ISIS/Base (use full option to write them)
• editing of linked compounds (in 3D browse mode) is synchronized with table

NEW features:

• command to generate grid maps from oblique crystallographic electron density maps. See make map m_xrayMap . This command enables ultra fast real space refinement.
• extension of the tools to generate atom type dependent property maps used for pharmacophore field generation and real space refinement. The generated grids ( g1 , g2 , .. up to g7 are used by the "gp" term.

  
  set type property {1.}
  make map potential "gp"
  

• 'File mode' for many operations in new Chemistry menu. (3D coordinates generation, conformation generator, and more )
• convenient GUI interface for contours of electron density maps;
• ability to save project in ICM 3.4 compatible format;
• GUI Dialog for joining (merging) tables
• GUI Dialog for sorting by multiple columns
• display gui "moledit" [off] [chem] # popups/hides the molecular editor window
• Askg() now supports the dialog syntax. Example:

  
  buf  = "#1 l_Passive_GUT_Absorption (yes)\n"
  buf += "#2 l_ToxCheck (no)\n"
  buf += "#3 l_hERG_QSAR (yes)\n"
  buf += "#4 l_Your_Model_Here (no)\n"
  
  Askg(buf)
  
  print $1, $2, $3, $4
  
  

• help for all functions. Just type the function name without parentheses, e.g. Shuffle and hit return.

Version 3.5-1a May 25, 2007

• import of 3D meshes in OFF file format;
• faster SVM classifier cross-validation;
• support for undefined and censored real numbers in arrays (import/export from strings, arithmetics,sorting);
• improvements in ICM Script Editor: "Save" button, saving/restoring the window size and position.

Version 3.5-1 May 20, 2007

Graphics & GUI:

• new hardware stereo for Sharp 3D LCD stereo monitors. It does not require any glasses!
• a workaround for problematic Intel graphics cards have been found
• individual clipping of skins and 3D mesh (grob) objects allows to open up surfaces without clipping of atoms inside.
• improved antialiasing for 3D graphics
• Three new styles for a beautiful display of chemical structures in xsticks : "chemistry" (showing bond orders), "chemplus" (bond orders,atom types and more) and "chemplusaroma" (aromatic rings) Controlled by the GRAPHICS.xstickStyle preference.
• In the "chemplusaroma" style: aromatic rings shown with circles or with thinner inner bonds (sounds funny :-) )
• new xstick/ball controls (ball/stick ratio, hydrogen/carbon size ratio, etc.)
• new manual torsion rotations: two halves of each rotatable chemical bond have rotation handles in the middle of each half. The bond rotation tool now allows this type of bond rotation.
• variable size of xstick balls. Depends on the van der Waals radius and controlled by preferences.
• triple bonds automatically oriented to the viewer
• transparent CPKs if xstick representation is displayed (allows to display both volume and chemical structure.
• improved transparency treatment and controls for skins and grobs
• easy movie making. It is now possible to make video in various formats (.mov, .avi, .mpg) on all platforms.
• new real-time ICM graphics grabbing engine allows to create simple movies from ICM sessions.
• Windows Only: Copy/Paste chemical structures,trees,alignments,plots in VECTOR format into any office application. That means that you can resize/adjust them without loosing quality.
• correct bond orders of amino acids directly assigned to the PDB objects (some ligands would still need to be fixed)
• fixing bond order of ligand in workspace with alternative positions works correct now (E.G: 1d4l)
• Automatically generated FORM view for chemical tables.(Ctrl+0)
  
• new hydrogen display mode button which toggles through 3 main modes (hide hydrogens, show polar hydrogens only, show all hydrogens);
• dynamic hydrogen bonds now available from the menu;
• +/- button controls for variable/stom/residue/variable label sizes;
• 'Copy image to clipboard' button for ICM graphics (+ supports antialiasing);
• Default location for quick images changed to s_outputDir (My Documents on Windows);
• slides: current object, grob clipping planes are now saved into slides;
• HTML-embedded dialogs now support pre-dialog commands;
• hydrogen bonds are undisplayed when undisplaying atoms they bind;
• dual-lighting for meshes;
• chain gaps are visualized in xstick and ribbon modes;
• allow to start rocking with a fixed number of cycles;

Chemistry:

• CIS/TRANS is preserved when displaying 3D molecules in 2D and when converting from smiles contaning '/' and '\' bonds.
• optimal orientation of chemical in table cells improved
• mol2 files can be ready as chemical spreadsheet. ( See read table mol2 )
• Fixed the problem with implicit hydrogens matching in make reaction command

New plotting engine in tables:

• SVG export;
• background shapes (rectangles, ellipses and polygons);
• new plot creation/editing dialog;
• zoom and translate controls;
• point size/bar width mouse control (right 5% of the plot area);
• more control over the colors including color gradient editor;
• selections in scatter plots and histograms;

Data anlysis:

• faster PLS regression tool;
• MAE(mean average error) statistics is shown for predictions (PLS/SVM);
• advanced clustering representative selection dialog;

Commands:

• write [macro] [s_file]
• read csv group ...
• read csv comment | mute ...
• Assign bond order from smiles or an existing chemical set bond topology as_ {s_smiles|X_chemical}
• Atom( )
• read distance ..
• move
• Index( center )
• Index( selection )
• Nof( [1] tree|auto )
• write movie ..
• l_beep = no #disable any beeps
• set slide name

Misc:

• site labels can be set to individual atoms;
• .icb files do not contain HTML tags anymore (which was causing Internet Explorer to show them as HTML);

BUG fixes:

• "Rename Column" validates the input
• Fixed crash in Match(...., i_field) (loadEDS "1atp")
• Fixed crash in S[ I ] = s
• Enabled writing ICM preferences is browser
• The secondary structure of sequences is now properly updated after 'Swap Branches' operation.
• Fixed image dimness after 'Center' tools
• Fixed distortion after objects were read in side-by-side stereo mode
• Fixed editing of rarrays in 'Preferences' dialog
• Opening multiple file does not affect subsequent calls of 'Open file' dialog
• fixed 'make grob image' for skins

Version 3.4-9d Feb 21, 2007

• Fixed problem with displaying surfaces on Intel graphics cards.
• Fixed problem with "invisible" selection marks and atom labels on Intel graphics cards.

Version 3.4-9c Dec 04, 2006

BUGS:

• Fixed crash in color cpk/write by by alignment
• Fixed "sticky" column selection in tables
• Default table sorting mode is switched to ascending

Version 3.4-9b Nov 21, 2006

NEW Features :

• ability to make reaction with multiple functional group mapping (--all|--only options). Multiple occurrences of a functional group
• atom selection is synchronized in 2D ligand view and 3D
• new "refmin" and "refmax" operations for group table by column command.
• Atom/Residue Font Edit Dialogs. Click on the Atom/Residue label button and hold for a second to get popup menu. Select "Font..." menu item to set font parameters.

BUGS:

• Fixed crash in Replace( s_ s_ simple )
• Fixed wrong chemical formula for charged metals

Version 3.4-9a Oct 25, 2006

NEW Features:

• contouring of electron density around atom selection added to the Tools menu ( Tools/Xray/.. )
• Map( m_ name ) function added.
• Table layout (row height,column width) now stores in ICB files
• File-Open can open multiple files. (Select with Shift and Control keys)
• Ability to sel color labels to tables rows. Press 1,2,3 .. to mark current row or selection. Alt+1,2,3 .. to select previously marked rows.
• Ability to edit multi lines text in tables cells. (Return - finish edit. Shift-Return - add new line)
• 'Lock' display mode for docking hits. Allows two view several compounds together in the pocket.
• 'Compare Chemical Tables' uses find table command.
• Ability to commit local change into Molcart.
  • Perform a query
  • Modify data in the result table
  • select modified rows, right click and choose "Update Database for Selected Rows"
  Command:

  modify molcart table=s_molcartTable T_localTable [column=S_colnames]

• antialiasing works for write image in high resolution mode too.
• New View Option for Sequence Alignment: 'Dot Similar Lettes'
• New way to edit/fix PDB bond orders, atom types and formal charges of ligands. You can use the "ligand view" in ICM workspace (open it by pressing the plus symbol) to perform simple ligand editing operations such as:
  • change bond order (move mouse to highlight the bond and right click for popup menu)
  • change atom type
  • change formal change
  • delete bond
• Ability to use R1,R2,... in the reaction filter. This allows to set additional conditions to the product symmtery.

  
    make reaction reac.rxn[1] name="res" rct.mol  filter="R1!=R2" 
    

• Ability to change (Ctrl+/Ctrl-) font size (title,axis,ticks) in the table plot. Default size is smaller.
• GRAPHICS.hbondMinStrength (default 1.0) preference introduced for Graphics. (range [0.-1.8])
• GRAPHICS.hbondAngleSharpness (default 1.7) preference defines the angular dependence of hbond. [1.-3.]
• contouring of electron density ( make grob m_ as ) bug for oblique crystallographic cells fixed.

BUG fixes:

• "Open With Password" did not work if file was saved with empty password. Fixed.
• Fixed problem in with cell editing. (Editor does not start on some keys. e.g digits)
• Tools panel was not shown by default in docking hit list. Fixed.
• 2D Ph4 search was broken for local tables in 3.4-9.
• File-Load PFam alignment works again.
• MolEdit: Copy As Smiles works correctly for reaction
• fixed bug in "make reaction". Multiple attachment points in reactant match were not processed properly Example:

  
    group table react Parray("[N;^3]([R1])[R2]>>c1ccc(cc1)N([R1])[R2]") "rxn"
    group table rr    Chemical( {"C1CCNCC1"} ) "mol"
    make reaction react.rxn name="rout" rr.mol
    

• Fixed a problem in common substructure matching algorithm ( find molecule sstructure ) which affected some cases with aromatic rings.

Version 3.4-9 Oct 14, 2006

NEW features:

3D display and representations:

• read mol [hydrogen] [type] [charge] # automatically set mmff charges upon reading a mol or sdf file
• building high quality images with write image: a new built-in antialiasing mechanism for both lines and triangles overcomes the limitations of the graphics card.
• new 2D labels, label popup menu , font/color control, e.g. "\Aa\A-helix"
• new 3D labels, 3D label popup menu, font/color control, e.g. "angle \AF\A"
• new dynamic distances (the 'labels' menu)
• shift atom and residue labels to the observer depending on the graphical representations
• Residue label drop down menu: shift residue labels to the side chain tips
• color by residue and atom (plus molecule object), e.g. color a_//c* as_graph object
• new hydrogen bonds. Now they are separate objects in workspace. Can be made between different objects and do not require conversion to ICM)

  make hbond a_1. a_2. display

  display hbondpairs {dot|wire|ball|label}

ICM Shell:

• Info(term) function to memorize energy term string
• authoring:

  write binary [all] s_file key=s_password [read only|comment]

  read binary [all] s_file [edit]

• rename x "y" auto # finds a unique name with the given root
• 'autoexec scripts' for icb files. Right click on the script and set "Auto-Exec" flag (Unix and unix are disabled this mode to prevent "viruses")
• Name( table, {column|header|selection} )
• Toupper( s|S 1 ) added to add 1st letter in every word.

Chemistry:

• Color chemicals by smarts pattern or atom filter select chemical t.mol {s_pattern|filter=s_cond} color=colorName|{r,g,b} [all|append]

  
  select chemical t.mol "[O,S&v2,N&^2&X2,N&^1&X1,N&^3&X3]" all append color=lightblue # color all hydrogen bond acceptors 
  select chemical t.mol "[!#6;!H0]" all color=lightred  # color all hydrogen bond donors
  

  See select chemical command.
• added exclude={s_sm|S_sm} argument for find molcart command which allows to filter unwanted groups.

  find molcart "C1=CNC(NC1=O)=O" exclude={"c1cocc1","c1ccccc1"} table="screenpub.chembridge" sstructure

• Rmsd( .. chemical ), superimpose chemical now fill R_out matrix
• multiple (up to three) labels in chemical enumerate and reaction
• Hydrogen Bond Acceptor/Donor Shortcuts in MolEdit.
• Ability to edit compound names in MolEdit.
• Conformation generator preserves compound names.
• Added 'Deep' mode for smarts count which allows arbitrary overlap.

  Nof( t.mol, s_smarts, atom )

GUI and Misc:

• "Refresh" menu item added to MolCart objects
• Added ability to change font color and boldness in alignment view.
• Added R/S button in moledit to toggle atom stereo labels
• Individual "editMode" for table columns.
• Single click in table plot activates the corresponding row.
• Added ability to change tab order (Drag'n'drop) for tables, alignments and htmls.
• Html windows can occupy "central" space
• Added Save&Quit Button for Moledit (when opened from table)
• Added GRAPHICS.keepResizeScale which control resizing GL window.

BUG fixes:

• Element name added to write pdb
• Cobalt treatment in read pdb "2d2g" improved.
• Fixed bug in chirality detection problem with explicitly drawn hygrogens
• fixed the problem with displayLock when adding rows.
• "Extract From ICB" works with filnames which contain dashes and other "illegal" characters
• refreshes sequence in GUI after mutate amino acid.
• Fixed crash in "read string s_url" for long URLs
• fixed crash in reading ccp4 maps under windows
• Fixed problem with ring closure after branch in SMILES parser
• "Extract From ICB" works with filenames which contain dashes and other "illegal" stuff

Version 3.4-8f Aug 22, 2006

FIXES

• add table1 table2 (adds correct values by column names)
• switching from between table tables enables "cursor action" on the cell even if cell was not changed.
• s_projectsDir added to preferenses
• fixed few bugs in recursive SMARTS [C;!$(C=O)]
• Insert Column Dialog: fixed Smiles( rxn )
• find molecule sstructure all (matches ring-no_ring atoms)
• fixed bug in skin area calculation

NEW features:

• ability to interrupt substructure search in molcart
• ability to define distance between groups in 2D susbstructure search (2D Ph4)

Version 3.4-8e Aug 15, 2006

FIXES

• fixed a few bugs in 'make reaction'. (Stereo were not preserved in reactants. Problems with reactant with explicitly attached hydrogens)
• GRID layout in table is saved in ICB file.
• Nof( chem, s_smarts ) allows overlap between fragments

FIXES

• color by molecule and by object
• fixed crash in MolEdit (random crash when moving mouse over the atom with an attachement point)
• fixed crash in iarray*integer
• deleting multiple plots
• fixed fonts sizes (zoom in/out) in scaffold view

Version 3.4-8c Aug 1, 2006

FIXES

• inconsistent row numbering when switching from GRID to TABLE mode.
• fixed memory corruption in pml->mm (after 'build hydrogen' and 'modify' where number of atoms increased pml->mm became inconsistent)
• double click splits tabs 50-50 (tables and alignments)
• random memory corruption in fingerprints
• minor bugs in aromatic -> kekule (5 member rings with o,s were not processed correctly)
• make flat did not work correctly with hydrogen attached to the stereo center.
• fixed problem with font size "jump" in the scaffold view.

NEW features

• 3D browse mode for tables (set property display [off] )
• Chemical( a_ exact hydrogen ) will preserve hydrogens
• MolEdit (Append To Table Auto/New)
• light settings moved into separate tab (save button added)

Version 3.4-8b Jule 21, 2006

FIXES

• The suffix (.png) was not appended to the file when saving molecule as image
• rename command is only called when the name actually changes
• Ctrl-E is focus-dependent now, Ctrl-A works in Linux (with Html documents)
• chemical names in SD files are consistent with changes in NAME_ column.
• Preferences values are stored correctly from "Edit Preferences" dialog.

NEW features

• Copy Molecular Image to album (right click in the chemical table)
• Assign Click/DoubleClick actions for chemical tables (Display/Display Lock)

Version 3.4-8a Jule 19, 2006

Bug fixes

• fixed edit-rainbow problem
• fixed adding multiple columns to molcart
• fixed bug in "[C;D1,D2]" (or similar) smarts patterns
• fixed z-rotate (double-click) in grid view

New commands

• Generating SAR tables

  
    make molsar chemtable coremol    # generate SAR table  
    

• Sort by multiple chemical columns

  
    sort t.mol1 t.mol2 [number]   # sorts by unique smiles. (by number of atoms with 'number' option)
    

Version 3.4-8 Jule 1, 2006

Graphics

• A better algorithm for transparent mesh/grobs was implemented. Control the transparency level with slides in the Advanced display tool bar. See also: GRAPHICS.
• Crop a mesh (grob) to make grobs with even edges (Right-click and follow the menu).

Document Editing and Linking

• support for both png and jpg images.
• drag and drop to the Edit Source window images, slides, viewpoints, scripts.
• The icm-html window supports the following syntax, some examples:

  
  <a href="#icm/slide/slideshow.slides/1"> Link text</a>
  <a href="#icm/script/scriptShellName"> Link text</a>
  <a href="#icm/viewpoint/vpShellName"> Link text</a>
  <img src="imgfileName" />  # the image needs to be in Workspace
  

• Individual Layout button at the bottom window status bar. This button memorizes the initial layout of an .icb file. It also allows to memorize the layout you like (click and hold, then follow the menu).

Shell and GUI

New preferences dialog. The preferences are now CONSISTENT BETWEEN VERSIONS.

Using the Soap client from ICM.

See soap .

New functions

• Sarray( s_wildCard directory ). See Sarray for details.

Chemistry

• Two types of pharmacophore searches implemented: chemical fragment based and based on pharmacophore centers (no vector directions for acceptors and donors yet).
• 3D chemical views for chemical tables. Now you can see and rotate each molecule a 3D sdf by double clicking.
• Also for 2D chemical tables, double click on a cell and rotate the molecule
• SAR tables. Chemical tables can have a core structure and be displayed as a scaffold

Edit Compound in a 3D pocket

Edit compound in place using a 2D editor and minimize it.

Alignments

• The 'hide'-pattern in multiple sequence alignments is saved to .icb files and restored upon reading.
• A new popup menu item for alignments allows to cut out a vertical set of sequence fragments

Bug fixes

• crash in Drag and Drop of files outside ICM to the Workspace fixed.
• the effect of disappearing characters in the terminal window upon cursor movements is fixed
• fixed bug with random changing of stereo configuration when making reaction.
• fixed bug with cutting single column from the table
• fixed bug in editing 3D ligands with c1cc[nH]c1 rings in moledit (missing proton)
• fixed bug in 'read ... "ftp://"'