ecepp

a force field used in the ICM program. The latest version is called ECEPP/3 was described in Nemethy et al. (1992). See also the following references: Momany et al. (1975), Nemethy et al. (1983)

fasta

program FASTA ( Pearson and Lipman, 1988 ) is used for search sequence databases, evaluate similarity scores and identify sequence similarities on the basis of local sequence similarity. The program is well suited for rapid database searches, because it does not handle insertions/deletions. In ICM, fasta also specifies one of the several allowed formats of sequence data storage and representation.

grob

an abbreviation for a general GRaphics OBject, which contains dots, and/or lines and/or solid surfaces; it can be a geometrical body, a contoured electron density, 3D plot, an arrow, etc. If the graphics object contains triangles, it can be represented by solid surfaces. The order of points in the triangles defines the direction of the normals which in turn defines which of the two sides are lit. Grob-file format is straightforward and editable.
To merge two or several grobs, use the double-slash operator (e.g. g = g1//g2//g3 ) or the write grob append command.
Example:

 
 read grob "icos"             # several example graphics objects 
 read grob "cube"             # are read in ... 
 read grob "oblate" 
 read grob "prolate" 
 gAll = g_cube//g_icos 
 
 display g_cube red           # ... and displayed 
 display solid g_icos blue 
 display g_oblate green 
 display g_prolate magenta 
 center

Setting property masks Creating grobs from molecular surface.This is done with the make grob skin command. In this command one can also specify the transparency level of the grob, e.g.


make grob skin a_2 a_2 0.6

Built-in filter functions for arrays, chemicals and table rows

Several ICM commands use functions to filter out table rows or database entries by an expression applied to a column/field value. For example: UNFINISHED

Built-in GUI functions for dynamic and user-defined dialogs in ICM.

To see how these functions are used, open the icm.gui file and search for a function of interest. Most of those functions are just used for internal ICM purposes and we were even hesitant to document or even list those. However some of them, e.g. nIcmObj are quite general and are frequently used.

These functions can be used in different expressions

AnimateViewMenu :
Apply : generates a so called 'modal' dialog with an Apply button, rather than the default Close button.
Atom : indicates if the level of selection (or a right click object for a popup menu) is atomic (see also Res , Mol , Obj )
AtomMenu :
canRestoreAutosave :
Cell :
CheckItem :
CheckModified :
ChemProperties :
ChemSearch :
ClusterDialog :
ConnectDB :
connected :
DisconnectDB :
Docking : yes, if the docking (D) license is present
EditLabelGrob :
EditMenu :
Energy : yes, if the energy (E) license is present
FileNew : a dialog
FileOpen : a dialog
hasLigandRedo : checks if the LIGAND.selection in 3D editor has 'redo' states.
hasLigandUndo : same for 'undo' states.
hasReceptor :
hasSwissID : see also set swiss
HelpBrowser :
Hidden :
Homology :
icongf :
isAmino :
isChemTable :
isCurIcm :
isDsGBox :
isDsMol :
isDsObj :
isGrobDot :
isGrobLabel :
isGrobSmooth :
isGrobTransparent :
isGrobWire :
isHet :
isHetnRes :
isIcmObj :
isLigandEdit :
isMini :
isNucl :
isObjFolder :
isPharm :
isReadOnlyMode :
isSeqNucl :
LearnDialog :
ligandUndo :
Mol :
molcartCanModify :
molcartCanRebuildIndex :
molcartconnected :
molcartHave3D :
MolEdit :
mysqldb : see also other molcart functions
nAsGraph :
nAtomInMol :
nBiomtMol :
nChemTable :
nDots :
nDsObj :
nDsSelObj :
Neighbors :
nGrob :
nLigAsGraph :
nLigAsGraphTerm :
nLigFrag :
nLines :
nMap :
nModel :
nObj :
nResInMol :
nSelSeq :
nSeq :
nStackConf :
nTable :
nTrianges :
nTriangles :
nUserObj :
Obj :
okToConvert :
PredictDialog :
Preferences :
QuickImage :
Quit : dialog :
Rebel :
RecentFilesMenu :
RecentPDBsMenu :
Res :
ResAtom :
SaveDir :
SaveProject :
Sel :
Selection :
SelectionLevelMenu :
SelectionModeMenu :
Seq :
TableToolsMenu :
Terms :
Toggle :
ToggleButton :
Upgrade :
Version :
Vls :
WindowsMenu :

hbond- hydrogen bonds

are calculated according to ECEPP/3 potential. One can also display hbonds with their distances, deviations from linearity, colored by the strength parameter which takes the angle into account.
Related commands are show hbond, display hbond, color, and undisplay .
See also: GRAPHICS.hbondWidth , GRAPHICS.hbondStyle

HTML documents in ICM

ICM can contain any number of html-pages. These pages appear in the shell as strings of the html property . To create an html document follow one of two possible routes:


read html "a.html"  # reads and sets the property mask
#
s = "<html><h1>TITLE</h1></html>"
set property html s

Internal tagsThe internal html documents can contain links to icm slides , viewpoints , images( both .jpg and .png ) and scripts with icm commands .

The shell objects representing slides, viewpoints, images and scripts can be linked to the html document with the following tags.


<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 album

In the graphics editor, these tags are automatically created when images, slides, viewpoints, scripts are dragged and dropped to the Edit Source window.