[ last-release ]
In this section we keep track of all the latest changes in different modules of ICM.
Version 3.7-2b Jun 23 2011
- added output= argument for all show commands which allows to grab the output for further processing.
- Improved rendering speed of xstick representation
- Fixed cis/trans depiction for R-group substituents in enumerate library
- Fixed memory few memory leaks when working with tables in macros.
- Fixed chemical formula generation for isotopes.
- copy/paste multiple cells from Excel into ICM spreadsheet.
- Fixed crash "Changing the final row in a filtered column crashes ICM" bugzilla: #697
- Fixed crash in pasting a column in the table with plot.
- XML parsing functionality. read xml, Collection, xml drugbank example
- fixed incorrect cis/trans bond interpretation in smiles. ( (\R)C=C -> R/C=C )
- new attachment point rendering style
- fixed "interrupted system call" error in read http.
- chiral centers with an R-group attached are correctly treated (stereo is preserved by parity) in make reaction.
- smiles property for sarray columns in the tables Toggles on-the-fly 2D chemical depiction.
- Fixed bug with non-preserving center of rotation in slides after clipping planes were moved. (also fixed in activeICM 1.1-5)
- Multi-receptor support in the 3D editor
- make reaction allows arbitrary R-group numbering
- multiple drag-able resize-able images in set background image command
- added 'Unlock ICB' function which clears read-only or password protection from ICB without reopening it.
- fixed few bugs in with password protected ICB files
- removing salts with modify chem delete salt
- preview for ICB files (Windows browser + ActiveICM)
Version 3.7-2a
- single quote string constant support.
- reader.icm script
- Logical(r|i|s)
- GRAPHICS.cpkClipCaps preference (1,2,3)
- SolveCubic( a,b,c,d | R_3|4 [all] ) => R, SolveQuadratic( a,b,c | R2|3 )
- fixed overlapping shaded and bordered boxes in alignment view. All view preferences now stored in ICB.
- WebKit integration is added
- other types of occlusion shading added ( TOOLS.occlusionColorStyle = "dark outside" or "light outside")
- fixed bug with opposite rotation of connected molecules/objects or grobs
- delete sequence nucleotide|protein|peptide
- fixed rdpdb for consecutive atoms with identical coordinates, e.g. 1a69, ds skin molecule,
- Nof( bond [error]) Nof( selftether [error] ), Select( selftether [error] ), Select( bond [error] )
- selftether treatment: set selftether , delete selftether , Srmsd( as selftether ), minimize "ts" , replaced tether= by selftether= in minimize montecarlo ; convert to set selftether
- improved convertObject (protonation of a_/U, minimize "ts" for the convert deviants)
- added output option for Rmsd and Srmsd function to store individual deviations into R_2out
- grouping by table column works with ND values correctly in aggregation operations.
- write gamess to write correct Z-matrix, memory limits.
- TOOLS.membrane, update icm.hdt, surfaceMethod="membrane" supported in Area( energy) and energy evaluations.
- bug with residue names for residue names starting from a leading blank after reading some pdbs fixed. (previously was breaking 1ytw,2i42,3f9a,2i4e,1kpe)
- CubicRoot(|)
- bug with crashes in find database fixed
- improving find database results (prioritize SC for HUMAN, ECOLI, BOVIN etc. in case of identical scores)
- a_J selection to filter short peptides.
- Name(sequences) returns an empty array (not error) when there are no sequences
- set column format supports internal ICM links.
- exclude and number options for learn atom command.
- set atom named fields is added
- anti-aliased and scalable fonts (atom/residue labels,etc) in 3D for windows and MAC
- Pattern( rs ), selections a_/Bbarcode_like_A12L2L and a_/Qbarcode
- translation to a destination point for a molecular and object selections (see translate )
- new 2D compound rendering option: color rectangles on hetero atoms instead of atom labels. See set property chemical view
- fixed crash in Askg
- new Iarray( a_// topology ) function
- new align sequence command (align number .. )
- new Select_by_sequence function
- find molecule sstructure drestraint ms1_inIcmObj ms2_inTheSameIcmObj added to set drestraints by chemical similarity
- delete link alignment ; link ms_ rewritten, many options added. autoLink action improved.
- join by structure column ignores hydrogens (3D can now be joined with 2D structures). stereo off option is added to ignore chirality.
- copy/paste and drag'n'drop between icm sessions ( images, molecular objects, meshes)
- build-tautomerand set-tautomercan be applied to HIS residues
- ND support for individual real values
- large 64 bit integer support for integer variables
- Grob( "cylinder", r_ra r_H )
- arbitrary length atom labels and ball radius (`set-label-atom and set-atom-ballcommand)
- search functionality in preference dialog.
- restore-preferencecommand is added (allows to set system preferences and variables to default values)
- date type is introduced
- new annotation style for alignments
- Charge/protonation state prediction using pKa model
- pKa predictions for bases and acids (`set-charge-auto command )
- GUI parser patched and icm.gui cleaned from in-line argument declarations to allow natural command syntax (the percent symbol, like %i_out , is no long needed ) in dialog descriptions
- option to avoid sampling His, Gln, Asn, etc. and hydrogens upon convertObject added (allows to keep atoms as is)
- concurrent multiple level contouring (with multiple colors) of distant density added
- read pdb improved to recognize unusual amino acids
- mmff treatment of two nitrogens in a fused aromatic ring improved
- set field can be used with alignments
- set color alignment is added
- Header(grob)
- make distance append behavior corrected (tool first order). Option make distance append P_atompairs .. added.
- superimpose P_atompairs os_movable command added
- set tether P_atompairs os_movable command added
- Area( grob error ) returns the percentage of unclosed area (to detect surfaces that are not fully closed)
- Volume( grob ) returns the percentage of unclosed area in r_2out
- copyMol, moveMol and jumping molecules
- not properly recognized chemical templates in 2D chem drawing
- unusual amino acids are not recognized ( 2jge )
- mmff treatment of two nitrogens in a fused aromatic ring problematic
- adding ligand (without receptor) to the table causes icm/C5H5N> processLigandSave Error> [2191] index 1 of array out of range [1:0]
Version 3.6-1i
- ND values properly handled in multi column histogram
- Fixed crash in molecular editor "Customize template dialog"
- Allow selection of mol column in Grid display of tables #480
- Copy table column into clipboard: skip unnecessary double quotes. #509
- Table grid layout ignores number format settings #505
- all htmls get deleted if a subset is selected and then deleted #499
- Transfer names from R-group tables in Edit.Ligand Tools.Find Group #416
- added superimpose to superimpose by atom pairs.
- fixed Copy/Paste of structures with attachment points to ISIS and ChemDraw #490
- fixed bug in Sort function. (original array was sorted)
- fixed bug in instability of ICM tree in some convert cases.
- fixed crash when one tries to merge two tables (certain combination of long column names is required ) #506
- fixed bug in add column function (overwriting an exiting column from macro). #507
- added "columnfilter", "tablesearch", "searchwindow" names for display window command to allow to launch corresponding GUI dialogs
- table sort is 'stable' (order of elements with equal keys is preserved)
- Sort indicator on real columns with ND or qualified values ( #497 )
- Rename of column header or edit of table cells doesn't invalidate session. Fixed ( #496, #253 )
- Toreal("ND") behaves as expected. ( #307 )
- Improve selection of points in graphs ( #488 )
- Rotation of molecule in the table cell does not change coordinates any more ( #495 )
- Fixed bug in copy/paste of table column containing ND values. ( #494 )
- added String( a_ pdb ) function #491
- GUI.busyCursorShowDelay GUI.busyCursorSyle to show "busy wheel" for long tasks
- fixed chemcolumn[:] index expression when column contains empty molecules.
- added source selection for 'Neighbours dialog ' (bug #486)
- added support of ND values for Min and Max functions.
- added TOOLS.smilesExportAsUnique preference which toggle canonical/unique smiles export for CSV and other formats.
Version 3.6-1h
- conversion to smiles and back might lead to loosing a chiral center (in some rare situations with compounds containing fused flexible rings)
- fixed bug in 'read http' when getting incomplete http header.
- correct order when reading fields from SD file
- sorting of columns with ND values is correct
- Copy / Paste of charge structures into ISIS/Draw crashes ISIS/Draw ( #463 )
- atom lists and some other properties are not displayed in reactions ( #462 )
- Substructure search for isotopes does not work ( #461 )
- 'Select conserved residues button' in alignment tools panel did not update graphical view. Fixed.
- fixed few problems with hidden block display/format in alignment view. ( #455 )
- added FTP.useHttpProxy preference which redirects all ftp requests through the HTTP.proxy (if non-empty)
- added support for native CDX clipboard format for direct copy/paste to ChemDraw
- fixed bug in aromatic to Kekule function. ( #452 )
- added new 2D depiction templates for bicyclo compounds
- fixed crash in copy ms_ "newName" for covalently bonded molecules.
- fixed crash when pressing ESC in pdb search tab (#447)
- optimized template loading procedure in 3D editor. (large template file are not affecting on the whole system performance anymore)
- fixed bug in filter expression of make reaction and enumerate library commands. (MolWeight,Nof_Atoms and some other functions were not working)
- fixed aromatic ring bond changing which may leads to wrong mmff typing in certain cases.
- added support for recursive SMARTS in the reactions.
- fixed ring connection in 2D molecular editor (#437)
- fixed bug in make reaction with all option. Added ring option to allow ring breaking. (#436)
- 'delete all' command is optimized for large number of objects
- macro 'cool' is optimized for large number of atoms
- MULTISEL option for f_fileName (`gui-programming) to allow select multiple file names
- Fixed type in icm.gui Chemistry.Convert.Structure to Smiles (uunique -> unique )
Version 3.6-1g
- fixed treatment of hidden fields in gui dialogs ( #413 )
- real arrays are also listed in Markush enumeration dialog.
- make molsar adds a scaffold used in the decomposition in the result table
- fixed leading space treatment in parsing 'extended real' values ( "<30." ">20." ) ( #414 )
- Fixed crash when right clicking on the selected atom in the molecular editor.
- add column function where function="Smiles(rxn,'asis')" works correctly for reaction column
- removed DOS style line ending in CSV export.
- changing order of tables,alignment and html pages by dragging works properly.
Version 3.6-1f
- 'delete off' property is supported for integers and reals
- 'delete off' property also protects from being overwritten during the project load.
- Added GUI.displayNDValueStyle preference to control appearance of ND (non-determined) values in GUI.
- Added clear pattern command and Exist pattern function to test/clear SMARTS search attributes
- searchSWS (search swissprot) works with a new protocol from www.uniprot.org/uniprot.
- 'ND' values are skipped in SDF export .
- TOOLS.onIcmExitMacro and TOOLS.onIcmStartupMacro are added. Allows additional customization of startup and exit. Read more .
- Markush enumeration works correctly when substituents have more than one attachment points
- Pressing 'Save Project' button (first time in unnamed project) and choosing an existing file did not ask confirmation. FIXED.
- Molecular editor: tool button after atom tools moved to the right side.
- alignment tool-bars was not refreshed after font size change. FIXED (#404)
- added keep option for make reaction command which preserves SMARTS attributes from the product part in the result table.
- Fixed bug in reading SDF/MOL files containing 'a' (any aromatic) atoms.
- Fixed bug in coloring structure by alignment if one of the chains contain non-standard residues.
- Speeded up xstick rendering for big proteins
- Fixed memory-leak in parray concatenation.
- Fixed problem in auto-recovery from crashes.
- added Ring function. (maybe used to return SSSR)
- Fixed bug in orienting molecules by scaffold. (numerical instability in certain cases)
- R-group decomposition works correctly for table selections. (#393)
- Fixed bug in R-group decomposition with 'Auto add -R-groups' option. (#391)
- Fixed broken layout in a few dialogs in GUI.
- Added 'BEGINGRID' and 'ENDGRID' properties for the GUI dialog description. It allows nicely arrange controls in a grid.
- Added "plotdialog" window name for display window command to launch a plot options dialog for the current table. (#390)
- Fixed incorrect behavior of backward/forward transitions in the html viewer (bug #389)
- Dialog created from the html link or by Askg function does not remember changed values on the next launch (bug #382). FIXED.
- Warning dialog at startup if license expire in less than TOOLS.licenseExpirationDaysWarning (default 7 days)
- new option all for Sarray( directory ) . Toggles recursive search on all sub-folders.
- Insert column dialog: disable 'OK' and 'Add To List' button when no appropriate function arguments can be found.
- New minimization routine in 3D editor.
- Receptor name is stored in the LIGANDS table in the 3D editor. Double-click will switch to the new receptor. Maps will be recalculated when needed.
- Meso forms are not detected as 'chiral' anymore. Added Label(chem,chiral) function which returns chiral labels for the set of compounds.
- make map potential .. cell= map
- contouring around a selection allows to clean distant density
- Fixed crash in R-group decomposition in empty entries.
- Fixed bug in write index command for files > 4Gb
- Default alignment of numerical columns is 'right'.
- Added explicit option to optimize exiting hydrogens in the receptor setup
- Added LIGAND.dockingFlexibleRings LIGAND.dockingPyramidalNitrogen preferences for 3D editor
- Inversion of R/S on rings can lead to inversion of the rings and not the substitutents. FIXED.
- Improvements in SOAP processing: Name Type.
Automatic casting to the ICM internal types. show/print for complex soap types. (bug: #346)
- Argument passing scheme for macros is changed to "by value". Adding '&' to before an argument in the macro declaration
toggles it to "by reference" (bug #340)
- if the first argument SoapMessage function contains name-space (ns1:myservice) it will be properly used further.
- fixed crash in Getarg() function when a long string was passed as a script argument.
- FlexLM package for Mac OSX + license find dialog.
- fixed disabling of ligand pocket surface button when all options were un-checked.
- added set label chemical and delete label chemical commands for annotation of 2D compounds in chemical spreadsheets
- Legend in plots is adjusted according to the current filtering.
- Lasso selection in molecular editor behaves exactly as in ISIS/Draw.
- Fixed incorrect behavior of txw_ field inside BEGINFRAME-ENDFRAME in GUI. (bug #334)
- Fixed unwanted modification of search pattern for Index( chem, chem sstructure function (bug #333)
- global option is added for the keep command. It forces to keep a variable all the way up through nested macro calls.
- Added warning for 'unprocessed' arguments in macro call (bug #331 )
- Added proxy authentication support. See HTTP.proxy
- read command supports user:password in URL for reading http pages which require user authentication
- Fixed stereo enumeration issue from 2D editor to 3D.
- Fixed crash in Askg function (bug #324)
- Fixed deletion of atoms in 3D editor if selection contains non-ligand atoms
- Fixed changing bond type for newly added fragments
- Fixed certain layout changing for slides which do not have "Apply Layout" property.
Version 3.6-1e
- set stack os_ loop|fast [off] # to memorize the object-stack display preferences
- auto option in the display stack os command.
- TOOLS.pdbReadNmrModels = "all stack" new preference introduced to read multiple NMR/Model conformations into a stored stack of a single object
- Cartesian stack handling for non-ICM objects to enable the read pdb all stack command for multi-model files.
- read pdb all stack to create a stack instead of explicit objects for a multimodel file.
- Fixed size changes of the plot area after command execution
- For reactions with multiple products separate column is create for each product in the result table
- Connect/Disconnect Molcart moved from "Chemistry" to "Tools" menu.
- new "Chemistry-Annotate by Substructure" is added.
- 'transparent' option is added for write png command which allows to save images with transparent background,
- new option 'all' for find pharmacophore command to score all possible mappings.
- new 'profile' view for alignments
- added new option 'output=' for _dockScan.
Version 3.6-1d
General :
- fixed issue with ribbon coloring for ATI HD2400 graphics card.
- fixed wrong interpretation of negation operator in SMARTS for two letter atom names. [!Cl]
- automatic redirection support is added for commands using 'http' protocol
- Added new options for column coloring in the 'Column Format' dialog.
- Selections a_//HD , a_//HA introduced for hbond donors and acceptors.
- the translate command expanded to support a coordinate matrix to specify the destination position, e.g. translate g_sphere Xyz(a_LIG.)
- Fixed bug in 'binding properties' skin.
- Fixed bug in set occupancy and set bfactor for multiple objects.
- Fixed bug with error treatment in nested macros.
- Ability to print 'table form view'
- Fixed problem with wrong 2D depiction of cis/trans adjacent to spiro system.
- New add option is developed for color grob by atom selection command to add the
GROB.atomSphereRadius parameter with the atom van der Waals radius.
- New pseudo option for color grob by atom selection to define areas of grob by distance from
lone pair centers around the hydrogen bonding acceptor atoms.
3D ligand editor:
- New 'Ligand Pocket surface' is added.
- 'Hydrogen Style' and 'Torsion' buttons are shared between 'ligand' and 'display' panel.
- R-Group template directory preference. Specifies directory where template SD files with R-groups are located.
- Fixed 'missing [H] in 2D view'
- R/S tool works with SP3 nitrogen.
- clicking with a 'bond tool' on an atom will build reasonable geometry for that bond. (Useful for double and triple bonds. E.g: for building peptide bonds)
- changing atom type sets charge to 0
- main undo/redo are hidden when ligand tab is active.
- added E/Z tool to switch cis/trans around double bond
- New 'Bond formation' tool is added. (Allows to make a bond between two disconnected atoms)
Version 3.6-1c Oct 5, 2008
New features and fixes:
- "Sample CIS/TRANS" option was added to the conformation generator.
- "Column Freezing" feature was introduced. Frozen column is always visible during horizontal scrolling.
- Text wrapping for long column names by underscore in GUI spreadsheets.
- Number of unique alternatives in the column filters is not limited anymore.
- Ability to store and re-apply "table views" (filters + hidden columns)
- Keyword (fulltext) search support for database files
- header support in read smiles
- Find in array
- New design of chemical search dialog. Saving DB search results in database files.
Appending search results to an existing table. See find molcart, find table
- Random sarray generation
- Ability to save tables as database files
- Support for zipped/gzipped files in make molcart
- Importing grobs in 3DXML format
- New commands for parrays: moving and deleting parray elements
- read table: replaced dependence upon global variable s_fieldDelimiter by optional parameter split
- "Columns plot.." dialog improved: additional functionality, more reasonable default arguments based on column types and selections.
Version 3.6-1b
Bug fixes:
- Restored the ICM script editing functionality in the HTML window
- Fixed the 'Neighbors...' > 'Undisplay Beyond Selection' crash
New features:
- Unique field support in database files
- Implemented adding columns and appending tables to tables in database files
- 'Select Diverse Set' dialog for molcart tables
- Added property recalculation support for some arithmetic operations
- Implemented setting column background color from the column format dialog
- Added 'Horizontal bars' style in plots
Version 3.6-1a
Bug fixes:
- Fixed bug with abnormal occupancy atoms display
- Fixed bug in GUI dialog for "Group by Column"
- Fixed bug in molecular editor. Connecting two rings though bond used to create two fragments.
- Fixed bug in pasting column. (wrong name was assigned)
- Fixed bug join command. (Column properties were not preserved)
- Fixed inconsistent behavior of the "Default Layout" button (toggling HTML, table, other windows)
- Fixed spurious window appearing when twiddling GUI.windowLayout in combination with "Default layout" button
- Fixed crash of calling "Query" on local databases with database browsing tables enabled.
- Fixed current item indicator in Ribbons menu and chain break property submenus.
- Fixed crash in "Extract from ICB" dialog.
- Array deleting protection extended to array element deletion command
- Assignments to table columns protected from wrong size array arguments
- Improved support for multiple slideshows in one session (correct current slide behavior)
New features:
- Gzipping (also gzipping in place) from ICM: compress binary extended with option filename= and option delete fixed for Unix.
- Exist( write | read | directory ) extended to establish directory/file properties. see code of loadEDS
- loadEDS extended to cash the electron density maps. Support for organization wide and local user repos. Variable TOOLS.edsDir introduced
- find_related_sequences macro : identifies all superposable pairs of chains in multiple objects
- calc_nosauc macro : calculates enrichment measures from an array of scores.
- makeAxisArrow macro : makes an axis object for a residue selection
- Added possibility to join one column from one table to another (Tools/Table/Add External Column(s))
- Ability to edit axis parameters for inline (cell) plots. Support for mutiple inline plots in the same table
- Added zoom by frequency axis in histograms.
- Added possibility to drag'n'drop Molcart table between databases.
- Added distance cutoff condition to local database 'Select Diverse Set' feature
- Added deleting protection for parrays (for example, image albums)
- Range customization for range (gradient) view in graphics window
- Support for logarithmic scales in histograms (for both value and frequency dimensions)
- Most chemical properties added through "Insert Column" store information about the way they were generated.
This allows to recalculate values in the dependent columns when source columns change for the following functions:
"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",
See also: add column function, build column
Version 3.6-1 Jul 3, 2008
New features:
- multiple data files in the command line are processed correctly; (icm file1.icb file2.icb)
On windows just drag multiple files on the ICM icon.
- occlusion shading to increase 3D perception of grobs (see color accessibility )
- chain assignment of system logicals, e.g. l_info=l_warn=yes
- one line semi-colon separated commands, e.g. a=1; b=2
- graphically interruptible script execution (run a macro and use graphics while it is running)
- new atom selections for ICM-converted objects: a_//E for hbond donors acceptors, a_//I for buried hbond atoms (requires show area ), a_//H for hydrophobs.
- store frame to create trajectory frames from a current conformation
- superimpose as_byTethers reverse # moves template rather than the selection, see superimpose
- superimpose rs1 rs2 residue # aligns residues as selected
- reading selected lines from large text files (emulation of the unix grep command piped to a reader): see read from file and the pattern= regexp option
- New selections for 3D editor: a_REC. (receptor); a_.I (Inhibitor or ligand) , a_.T (Templates), a_./R rotatable residues, a_./L ligand pocket residues.
- directory TAB-prompting from the ICM command line
- fast Sphere function and symmetry generation, updated findSymNeighbors macro
- copy ms s_newobj
- modifyGroupSmiles macro allows to modify any terminal atom in ICM objects regardless of the tree.
- new short view for a table with families of rows (see set group column ).
- re-linking an alignment to selected molecules WITHOUT re-linking sequences (see option only )
- interruptibility of hydrogen bonding optimization, and other long procedures
- new, simpler style for the workspace ( see GUI.workspaceStyle )
- widescreen window layout style: see GUI.windowLayout
- modifications to support name and format changes in new 'remediated' PDB as well as the old PDB
- finding atoms flanking abnormally long bonds and backbone chain breaks, see Select( as_ delete )
- GUI for the chain gap style and label style in the Ribbon drop-down menu
- indexing mmcif files from pdb and converting them to chemical tables
- Adaptive superposition (see below) and rmsd calculation for a subset, r_out and r_2out (see superimpose minimize)
- Now all graphical layers (planes) both active and inactive are saved into .icb
(previously the info about not displayed layers was lost)
- exitSeslogStyle introduced to allow to save a short version of user command history
- Ability to color sequences in alignments by secondary structure
- When printing alignments, groups are not split between pages, when possible
- Window caption redesigned to make the content more visible when ICM window is minimized
- New scatter plot styles: connected, bars, triangles.
- Connected plots colored by discrete value column can be used to make multicurve plots.
- Support for ND values in plots
- Logarithmic plots
- Separate zooming by each axis: left-click+mouse up/down on axes. Zooming is centered at the click position on the axis.
Zooming and translations in histograms..
- Wheel zooming in plots
- New plot item: matrix (used in interactive Ramachandran plots)
- Filter for plots: ability to show only some rows
- Label options in plots: point labels, labelOnSelect
- More control over plot scales: user-defined steps
- GUI interface to Protect/Unprotect shell objects/variable
- sequences can be protected from deletion ( see set property delete off )
- 'Virtual' grouping by column
- 3D ligand editing tools.
- named selections can be stored in the ICB file.
- Background images in graphics window
- Slide blending effect is grabbed into movies with its natural frame rate
- Context menu in graphics window
- Support for materials and textures in grobs: Wavefront OFF import/export, workspace menus, material editor
- Improved clustering representative selection
- New ribbonStyle ="smooth ribbon"
- 'Reload' button in ICM manual
- Faster rotation initiation of huge grobs (previously there was a lag)
- Allow rotation in the opposite direction by setting negative speed in the Rocking/Rotation preferences dialog.
- Saving the whole image album into a certain directory. Available through right-click on album. See also write image parray.
- Insert column dialog: fast option to add columns at the end of the table
New commands/functions:Functions for chemical enumeration. scaffold is a chemarray of one element with R1,R2,.. points:
- color accessibility grob r_depth # shades deeper parts of a surface/mesh.
- set type charge mmff # a combined version
- a_//I a_//E a_//H selections for ICM objects (see as_byproperty )
- term shortcuts for show energy, minimize and montecarlo, e.g. "mmff","map","energy" (see terms )
- show area born : to calculate accessibilities with temporarily enlarged radii (one at a time).
- display stack for interpolated animation of stacks.
- Color(M_rgb) returns sarray of color names.
- Selecting by number, e.g. select molecules by number of residues in them,
or select objects by number of molecules in them.
- set tether residue rs1_ rs2_ : to force a simple sequential residue alignment (instead of looking at residue numbers of performing sequence alignment)
- Moment( [pca|simple|all]) returns principal moments of inertia
- Min( M1 M2) , Min( R1 R2) , Max( M1 M2 ), Max( R1 R2 )
- selection for the residue label atoms: a_//L
- selection for secondary alternatives in a PDB file: a_//AS .
Previously we had to say something like a_//Ab,Ac,Ad,A2,A3 that was not correct in some cases.
- read anything pattern= s_regexp # equivalent to external unix pipe with grep: read sarray unix grep ...
- The Sphere function can return the desired level of selection:
Sphere([Mxyz|as] as radius object|molecule|residue )
- "ts" term for self tethers. ALso needs selftether= as_ argument. To switch tethers-to-self (ts) for a selection of atoms, use: set tether
- TOOLS.pdbReadNmrModels preference to force read pdb to read all NMR models.
- TOOLS.tsWeight parameter to the weight of the self-tether function.
- TOOLS.tsToleranceRadius parameter to the weight of the self-tether function.
- TOOLS.minSphereCubeSize parameter to controlled the accelerated Sphere function.
- os_ ms_ rs_ and as_ selections with index expressions, like a_* [1] will now return an empty selection if the index is out of range.
- New commands to hide the stack inside an object. See load stack object store stack object , delete stack object . Option store for montecarlo, option stack for set object . Nof|Exist( os1 stack ) .
- the build string command extended to allow multiple molecules and both one-letter and three letter code (e.g. build string "AGT,HH" or build string "nter ala cooh;nh3+ gly gly coo-" )
- Syntax extensions: dollar expressions with table header members are now allowed, e.g. $T.name .
- read table html ICM will parse an HTML table, get rid of the HTML tags and read it into an ICM table.
- build atom command for 3D chemical editor
- Trim ( seq S_tags ) a function to remove protein tag sequences.
- Trim ( s S_regexp2delete ) a function to remove a list of regular expressions
- Srmsd( ms1 ms2 matrix ) function to return optimal Srmsd and M_out with cross molecular srmsds.
- Link chemical array to some R-group in the scaffold
- : link group
-
Nof( scaffold library ) ⇒ total library size
-
Nof( scaffold group ) ⇒ Iarray of substituent sizes
-
Chemical( scaffold I_pos enumerate ) ⇒ get one chemical
- Name object parray
- Simple linear regression models: LinearModel
- Functions to interpolate colors
More functions.
- Box( R_6box r_margin ) expands or shrinks a box
- set group column t.colname [off] # to group by sorted column value
- link ms_ ali only # relinking alignment to a molecule
- GUI.workspaceStyle defines two different workspace styles
- s_pdbDirFtp and s_pdbDirWeb to control the sites for download with pdbDirStyle 6 and 7 accordingly.
- Name( string [ html | command ] ) returns the list of html objects or scripts in ICM shell
- Select ( as smooth|hydrogen|hbond ) : expand selection with bonded terminal atoms
- Select ( as bond nNeighbors ) : select by the number of bonded atoms
e.g. Select( a_ bond 1 ) returns terminal atoms
- Select ( as fix | unfix ) : select atoms on rotatable or fixed branches
-
read table mmcif s_file # from mmcif to a chemical table
-
write index mmcif s_mmcif_file # generate an index file for an multi-entry mmcif
- exitSeslogStyle for short seslog files
- superimpose minimize . superimpose ... minimize # adaptive superposition with iterative re-weighting
- Rmsd(... minimize)
- TOOLS.superimposeMaxIterations TOOLS.superimposeMinAtomFraction TOOLS.superimposeMaxDeviation parameters for the minimize option of the superposition.
-
Srmsd( ms1 ms2 as1_subset .. )
# equivalences from , rmsd number from as1_subset.
-
Select(rs margin i_marginSize)
function to expand selections along the chain. e.g. Select( a_/4,44 margin 2) will return a_/2:6,42:46
- convert as_newRoot # in place rerooting of hetam molecules (will not work for peptides)
- write index mol2 "file.ml2" # added to allow easy indexing of mol2 files
-
write index pattern=s_separator [add=s_prefix] s_file
-
write index [fasta] file.fas
- Image, Info image
- texture support for grobs: Image, Property, set texture
- Setting images to background (+ in GUI):`set-background-image
- Gzipping from ICM: compress binary
- Testing file identity: test binary
- read table html with the simple option processes more HTML entities, like gt,lt,amp,nbsp
- slide layout string function
- list molcart connections
BUG fixes:
- undisplay skin bug fixed
- display skin molecule for a non-current object bug fixed
- disconnected molecules not merged anymore for some non-standard pdbs without chains (e.g. 1xwk 1ssq 1xt8 )
- unnecessary output in writing multiple objects (and command align) with l_info=no suppressed
- fixed problems with opening files containing commas in the file name
- fix 'undisplay window=s_' when no graphics shown
- crash in reading mol2 entries via index when the index does not exist fixed
- fixed: 'make map potential "gc" simple'
- incompatible parray assignment disabled #chem[1] = seq
- removed trailing spaces in Label( as_ | rs_ )
- fixed: 'color volume black'
- fixed: 'delete alias'
- fixed listing binary contents for files with names "a.icb" and "v.icb"
- fixed 'set sstructure' to return error on buffer sequences
- fixed bug with reading binary files containing slides + 2D labels
- fixed bug with 'make hbond' not supporting r_maxDist
- fixed deleting table folder in GUI to keep slides and layout tables.
- remove length limits for icm.gui items
- fixed: re-reading sequences from ICB used to produce duplicate sites
Version 3.5-1r
- Fixed number of issues in mol2 protein reader.
- Askg returns correct values in muti-tab dialogs.
- Fixed unexpected behavior in make reaction when salt or counter-ion matches a reactant.
- Fixed bad interpretation of four slashes in html pages
- Fixed problem with comma "," in file path in openFile macro (backported from 3.6 version)
- Fixed "cursor jumping" when editing smiles in 'ch_' input
- Added support for non-tetrahedral chirality (E.g: cis/trans bond configuration around the ring)
- Added color by object_C into GUI. Also added possibility to color only carbons in the selection with a custom color.
- Added Index unique elements function to return indices of unique elements
- Fixed several issues in 2D pharmacophore search
Version 3.5-1q
- Fixed chemarray[ I_index ] = chemarray assignment
- maximum name length for molecular objects is increased to 64.
- fixed trimming object names from the beginning.
- fixed bug in findPDB macro
- Added set resolution command.
- Fixed memory leak in chemical library enumeration
- Added TOOLS.sdfStereoParityOutput logical variable which controls stereo parity output in SDF/MOL files
- Fixed atom stereo parity calculation in MDL MOL files.
- Fixed resize problem in GUI. (bottom of the tables/alignments could go out of the range of the screen)
- add table performs conversion of column types.
- Added support for 'ND' values into table column filters.
- Added "Page Setup" dialog for table printing. ( autofit option )
- Fixed crash in Askg function
- Fixed 'Reorder table by Cluster' crash
- In make reaction fixed bug when reactant has an R-group attached to the chiral center.
- In R-group decomposition and reactions R1,R2 matches implicit hydrogen by default.
- Fixed preservation of 'ND' values in some commands and binary read/write.
- Fixed selection updates in plots after "Select Marked Rows".
- Fixed "Search for Browser Pro License.." dialog item in Molsoft Browser.
- Fixed few CIS/TRANS issues when editing 3D molecule and 2D depict from 3D.
- New 'pause' option in display rotate.
Version 3.5-1p Apr 16, 2008
- Extract Ligand 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 restoring single/double bond order from aromatic systems with exocyclic double bond
- rename table checks if all columns can be renamed before actual renaming 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 to 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 # re-contour 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:
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:
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 kernel 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 anti-aliasing 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 anti-aliasing);
- 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 containing '/' 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 analysis:
- faster PLS regression tool;
- MAE(mean average error) statistics is shown for predictions (PLS);
- 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:
BUG fixes:
Version 3.4-9 Oct 14, 2006
NEW features:
3D display and representations:
ICM Shell:
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 preferences
- 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 substructure 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 attachment 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 (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 to 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
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
Shell and GUI
New preferences dialog. The preferences are now CONSISTENT BETWEEN VERSIONS.
Using the Soap client from ICM.
See SOAP services for more information.
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://"'