[ CONSENSUS | CONSENSUSCOLOR | FILTER | FTP | GRAPHICS | GRID | GROB | GUI | IMAGE | LIBRARY | OBJECT | PLOT | SITE | TOOLS | WEBLINK | WEBAUTOLINK ]

 
 IMAGE.color = yes       # this member is a logical  
 IMAGE.stereoBase = 2.5  # redefine real distance between stereo panels 

CONSENSUS

The consensus symbol is established if the percentage of specified residues in a give column exceeds the fraction given in the 2nd column. In rows were we provide two symbols (e.g. "-n"), the first (e.g. '-') is used in alignment representations, while the letter form of this symbol (e.g. 'n') is used in residue selections, (e.g. a_/Cn ) The first matched consensus condition takes precedence. In an example below, if Q is found in more than 85% or sequences, its consensus symbol is Q, if the percentage is between 60 and 85, the symbol becomes q, and if no consensus is establish, the symbol becomes the dot character ('.').

 
#>T CONSENSUS 
#>-symbol------fraction----residues--- 
   A           85          A 
   C           85          C 
   Q           85          Q 
... 
   d           60          ND 
   -n          70          ED 
   +o          60          RK 
   gj          60          G 
   q           70          Q 
   p           60          P 
   t           60          TSN 
   "#h"        85          WLVIMAFCYHP 
   %f          65          WLVIMAFCYHP 
   " g"        85          - 

 
#>T CONSENSUSCOLOR 
#>-residue-----color-------symbols---- 
   *           *           *         # separator between sections 
   ED          "#ff0000"   "-EDp"    # E and D residues will be colored red under '-','E' or 'D' 
   KR          "#0000ff"   "+KRp" 

[ FILTER.Z | FILTER.gz | FILTER.uue ]

 
 z = "pcat %s"     # define the action for the unix packed files  
 group table append FILTER header z  # append new filter to the structure  

 
"sed 's:begin .*:begin 600 /tmp/UUPtm:' %s | uudecode && cat /tmp/UUPtm && rm -f /tmp/UUPtm" 

[ FTP.createFile | FTP.keepFile | FTP.proxy | HTTP.proxy | HTTP.ignoreProxyDomains ]

String format: ftp.proxy.host.com[:port]

String format: [user[:pass]@]http.proxy.host.com[:port]

HTTP.ignoreProxyDomains

string with ';' separated list of domains where HTTP.proxy should not be used.

Example:

HTTP.ignoreProxyDomains = "localhost;*.molsoft.com" # local host + everything which ends with .molsoft.com 

GRAPHICS

[ GRAPHICS.alignmentRainbow | GRAPHICS.atomLabelShift | GRAPHICS.atomValueCircles | GRAPHICS.ballRadius | GRAPHICS.ballStickRatio | GRAPHICS.clashWidth | GRAPHICS.chainBreakStyle | GRAPHICS.chainBreakLabelDisplay | GRAPHICS.clippingPlane | GRAPHICS.clipStatic | GRAPHICS.cpkClipCaps | GRAPHICS.displayLineLabels | GRAPHICS.displayMapBox | GRAPHICS.dnaBallRadius | GRAPHICS.dnaRibbonRatio | GRAPHICS.dnaRibbonStyle | GRAPHICS.dnaRibbonWidth | GRAPHICS.dnaRibbonWorm | GRAPHICS.dnaStickRadius | GRAPHICS.formalChargeDisplay | GRAPHICS.grobDotSize | GRAPHICS.grobLineWidth | GRAPHICS.hbondStyle | GRAPHICS.hbondRebuild | GRAPHICS.hbondMinStrength | GRAPHICS.hbondAngleSharpness | GRAPHICS.hbondBallPeriod | GRAPHICS.hbondBallStyle | GRAPHICS.hbondWidth | GRAPHICS.sketchAccents | GRAPHICS.hetatmZoom | GRAPHICS.hydrogenDisplay | GRAPHICS.light | GRAPHICS.lightPosition | GRAPHICS.mapLineWidth | GRAPHICS.occupancyDisplay | GRAPHICS.occupancyRadiusRatio | GRAPHICS.quality | GRAPHICS.rainbowBarStyle | GRAPHICS.resLabelDrag | GRAPHICS.resLabelYShift | GRAPHICS.ribbonCylinderRadius | GRAPHICS.ribbonGapDistance | GRAPHICS.ribbonRatio | GRAPHICS.ribbonWidth | GRAPHICS.ribbonWorm | GRAPHICS.rocking | GRAPHICS.rockingRange | GRAPHICS.rockingSpeed | GRAPHICS.selectionLevel | GRAPHICS.selectionStyle | GRAPHICS.stereoMode | GRAPHICS.stickRadius | GRAPHICS.surfaceDotSize | GRAPHICS.surfaceDotDensity | GRAPHICS.surfaceProbeRadius | GRAPHICS.transparency | GRAPHICS.wormRadius ]

GRAPHICS.alignmentRainbow

alignment rainbow that can be used to color positions in the alignment by a custom array. To see colors and their names run the makeColorTable macro. Example:

read binary alignment s_icmhome+ "example_alignment.icb"
GRAPHICS.alignmentRainbow = "pink/white/lightblue/yellowgreen"
set field alig Random(0., 1., Length(alig) )  # will set the last item in color menu
# another possibility
set field alig 1 "random_colors" Random(0., 1., Length(alig) )  # 1st user field

See also: set color ali ; set field ali field_name R ..

GRAPHICS.atomLabelShift

a non-negative integer number of spaces preceding an atom label. This parameter is useful for displaying labels next to a solid representation, such as xstick or cpk.

See also: GRAPHICS.resLabelYShift Default (0)

GRAPHICS.atomValueCircles

GRAPHICS.atomValueCircles allows one to display a circle with a positive value on every atom for those atom fields:

1. = "none"
2. = "field"
3. = "b"
4. = "occupancy"
5. = "area"

The radius of the circle and the value tranformation upon changing hydrogen display is defined as follows:

• "field" shown as is, the values from undisplayed hydrogens are accumulated
• "b" radius is the b-factor value divided by a 100.
• "occupancy" shown as is
• "area" radius is the b-factor value divided by a 40., the values from undisplayed hydrogens are accumulated

The Escape button resets the preference to "none".

Example:

show surface area a_
set area a_//n* 100.  # just to show that it can be custom set as well
GRAPHICS.atomValueCircles = "area"
display new

GRAPHICS.ballRadius

radius (in Angstroms) of a small ball displayed as a part of ball or xstick graphical representations of a molecule.
Default (0.15)

GRAPHICS.ballStickRatio

A default ratio of ball and stick radii. This ratio is applied when the styles are switched from the GUI xstick toolbar.
Default (1.4)

GRAPHICS.clashWidth

relative width of a displayed clash . This parameter can be changed from the File/Preferences/DisplayGeneral menu.
See also: lineWidth , GRAPHICS.grobLineWidth , GRAPHICS.hbondWidth , GRAPHICS.mapLineWidth , lineWidth .
Default (1.)

GRAPHICS.chainBreakStyle

controls how missing residues in a missing protein fragment are displayed (in ribbon style). Now the gaps can be ignored or shown as ribbon bullets. Thus, available choices are the following:

1. = "none" # nothing is displayed
2. = "bullets" # gap is show as bullets, the number of bullets depends on the number of missing residues

Individual treatment of the chain gap display.The ribbon chain break display can also be suppressed at the molecular level with the set property "nobreaks" command, e.g.

set property "nobreaks" a_1

See also:

• GRAPHICS.chainBreakLabelDisplay
• ribbon
• Select( rs delete ) # detects atoms flanking a chain break

controls how the number of missing residues in a missing protein fragment is displayed (usually as a ribbon ). ICM tries to draw one bullet for each missing residue. In the auto mode the label is displayed only if the number of bullets is different from the number of missing residues.

1. = "none" # the label is not shown
2. = "all" # the label is always shown.
3. = "auto" # shows label if N bullets != N missing residues

See also: GRAPHICS.chainBreakStyle

GRAPHICS.clippingPlane

parameters set/returned by the center plane command. See also:

• GRAPHICS.clipStatic

GRAPHICS.clipStatic

GRAPHICS.cpkClipCaps

preferences to control the way the cpk spheres are being displayed when cut by a clipping plane.

1. = "none"
2. = "stencil" <-- default
3. = "explicit"

Both capping methods have some side effects and slow down the graphics performance. User discretion is advised. See also:

GRAPHICS.displayLineLabels

enables/disables the display of edge lengths (inter-point distances) of a grob generated with the Grob( "distance" .. ) function. This parameter can be changed from the File/Preferences/DisplayGeneral menu.
See also: Grob ("distance" .. )
Default (yes)

DNA bases in ribbon representation are shown as balls controlled by the above real parameter. You can undisplay them with the: undisplay ribbon base command.
Default: 1.5

GRAPHICS.dnaRibbonStyle

GRAPHICS.dnaRibbonStyle = "complex shapes" a method of schematic/simplified representation of DNA or RNA in which the bases are shown as:

1. = "ball"
2. = "flat shapes"
3. = "complex shapes" <-- current choice

a preference regulating the formal charge visualization of the visible atoms:

1. = "none" : do not display formal charges
2. = "all" : label all formally charge atoms
3. = "integer only" : skip fractional formal charges
4. = "ligand only" : do not display charges on polymers, display them only on 'hetatm' compounds

See also:

• GRAPHICS.occupancyDisplay

GRAPHICS.grobDotSize

default radius of a dot/vertex in a grob.

See also: lineWidth , GRAPHICS.grobLineWidth

Default: 3.0.

GRAPHICS.grobLineWidth

relative width of displayed lines of 3D meshes ( grobs ). Also affects the interatomic distance display. This parameter can be changed from the File/Preferences/DisplayGeneral menu.
See also: lineWidth , GRAPHICS.clashWidth , GRAPHICS.hbondWidth , GRAPHICS.mapLineWidth .
Default (1.)

 
 GRAPHICS.hbondStyle = "dash" 
        1 = "dash"      # the default choice. Just a line 
        2 = "length"    # show the D-A distance in addition 
        3 = "length and angle"  # show both the distance and the 180. - <D-H.. A> angle 

This preference determines if the Graphics user interface (GUI) hbond button will display hydrogen bonds dynamically (the bonds will change as the coordinates change), or a parray of pairwise distances will be generated separately. It also regulates if intramolecular bonds are suppressed.

1. "static"
2. "dynamic"
3. "intermolecular"

See also:

• make hbond
• display hbond
• Table(distobj distance)

GRAPHICS.hbondMinStrength

GRAPHICS.hbondMinStrength parameter determines the hbond strength threshold for hbond display. The strength value is between 0. and 2. By changing 1. to 0.2 you will see more weak hydrogen bonds.

This parameter can be changed from the GUI hbond button popup-menu.

See also: GRAPHICS.hbondAngleSharpness Default: 1.

GRAPHICS.hbondAngleSharpness

GRAPHICS.hbondAngleSharpness determines how the strength depends on the D-H...A(lone pair) angle. The preference can be found the general Preferences menu

Default: 1.7

GRAPHICS.hbondBallPeriod

This parameter defines the distance between centers of spheres of hbonds divided by the diameter of the sphere.

GRAPHICS.hbondBallStyle

GRAPHICS.hbondBallStyle parameter controls the size of the hbond spheres and the gradient of those sizes. The master size is a fraction of the GRAPHICS.ballRadius .

The following possibilities are implemented:

1. = "even" : all hbond-spheres have the same size
2. = "telescopic" : a zoom from donor to acceptor
3. = "by energy" : better hbonds are shown with thicker spheres
4. = "by atom size" : the radii form a gradient between ball radii of the hbonded atoms.

GRAPHICS.hbondWidth

relative width of a displayed hbond . This parameter can be changed from the File/Preferences/DisplayGeneral menu.
See also: lineWidth , hbond display hbond, GRAPHICS.grobLineWidth , GRAPHICS.clashWidth , GRAPHICS.mapLineWidth .
Default (1.)

logical GRAPHICS.sketchAccents if yes , activates a drawing mode that highlights the boundaries of objects with black accents. It generates a Edouard Manet type visual effect (e.g. Olimpia, 1863). Example in which the current object is shown as ribbon with ligands in cpk and surrounding side chains as xsticks:

  GRAPHICS.sketchAccents = yes
  GRAPHICS.ribbonWorm = yes
  GRAPHICS.wormRadius = 1.
  GRAPHICS.quality = 20
  GRAPHICS.stickRadius = 0.25
  GRAPHICS.ballRatio = 1.1
  GRAPHICS.transparency[1] = 0.6
  GRAPHICS.hetatmZoom = 1.1
  color background white
  color residue label black  # if you decide to display them
  display ribbon white
  display a_H cpk magenta
  display a_H xstick
  display Res(Sphere( a_H a_!H,W//!c,ca,n,o,h*  )) & !a_*.//n,o,h* xstick white
  color xstick a_!H,W//n* lightblue
  color xstick a_!H,W//o* lightpink
#  display residue label a_//DX

 
 GRAPHICS.hydrogenDisplay = "polar" 
        1 = "all"   # all hydrogens are shown 
        2 = "polar" <-- current choice  # polar displayed, the non-polar hidden 
        3 = "none"  # no hydrogens are displayed 

 
display new reflection 

 
build string "se his trp glu" 
display cpk 
color background blue 
GRAPHICS.light[5:7] = {0.2 0.2 0.6}  
display new reflection 

GRAPHICS.lightPosition

X,Y and Z posiion of the light source in the graphics window. The X and Y coordinates are usually slightly beyond the [-1. 1] range where [-1.,1.] is the size of the window, and the Z position is perpendicular to the screen and is set to 2. (do not make it negative). The default values are the following:

GRAPHICS.lightPosition = {-1.,-2.,2.}

GRAPHICS.mapLineWidth

relative width of lines and dots of a displayed map . This parameter can be changed from the File/Preferences/DisplayGeneral menu.
See also: lineWidth , GRAPHICS.grobLineWidth , map , GRAPHICS.hbondWidth .
Default (1.)

GRAPHICS.occupancyDisplay

preference controlling if and how the partial or zero atom occupancies are displayed. The abnormal occupancies are shown as circles around atoms. These following values are allowed.

1. = "none" # nothing is displayed
2. = "circle" # a circle is displayed
3. = "label" # a circle and a label with the value (zero values are not shown)

A silly example.

 
GRAPHICS.occupancyDisplay="label"
build string "se ala his"
set occupancy a_//n* 0.5
display xstick

See also:

• GRAPHICS.occupancyRadiusRatio
• GRAPHICS.formalChargeDisplay

GRAPHICS.occupancyRadiusRatio

The radio of a circle showing non-1. occupancy atoms to the van der Waals radius of the atom.

Default value: 1.5

See also:

• GRAPHICS.occupancyDisplay

GRAPHICS.quality

integer parameter controlling quality (density of graphical elements) of such representations as cpk, ball, stick, ribbon . Do not make it larger than about 20 or smaller than 1. This parameter supersedes the previous ballQuality parameter.
We recommend to make this parameter at least 15 if you want to make a high quality image. You can also increase the number of image resolution by making the image window 2,3,4 times larger (in the example below it is 2 times larger) than the displayed window.

 
GRAPHICS.quality = 15 
display ribbon 
 
# press Ctrl-D  for the fog effect, move clipping planes, change fogStart 
 
write image png window=2*View(window) 

1. = "left" <- default choice
2. = "right"
3. = "no text"
4. = "no bar"

GRAPHICS.resLabelYShift

a non-negative integer number of spaces preceding a residue label that shifts it to the right (Y axis). This parameter is useful for displaying residue labels next to a solid representation, such as xstick , ribbon or cpk.

See also: GRAPHICS.atomLabelShift, GRAPHICS.resLabelDrag and s_labelHeader

Default ( no ).

GRAPHICS.ribbonCylinderRadius

GRAPHICS.ribbonCylinderRadius is the real radius of helical cylinders in schematic protein topology display for the ribbonStyle = "cylinders" preference.

The radius can be set to zero for an automated, variable-radius mode or to a specific radius. Example:

read pdb "1crn"
ribbonStyle = "cylinders"
GRAPHICS.ribbonCylinderRadius = 2.2
display ribbon

See also:

• ribbon
• ribbonStyle

The minimal distance between the first atoms of the neighboring residues when the ribbon gap will be drawn if l_breakRibbon logical is set to yes. You can also control the display style of gaps with the GRAPHICS.chainBreakStyle variable.

Default: 4. See also: GRAPHICS.chainBreakStyle

GRAPHICS.ribbonRatio

real ratio of depth to half-width for the protein ribbon .

Warning: note that this parameter influences GRAPHICS.wormRadius if GRAPHICS.ribbonWorm is set no no . In this case GRAPHICS.wormRadius will be redefined as GRAPHICS.ribbonWidth * GRAPHICS.ribbonRatio automatically.
Default: 0.3

See also: residue field "_WORMRADIUS_" for variable ribbon radius of the worm representation.

See also: residue field "_WORMRADIUS_" for variable radius of the worm representation. Example:

read pdb "1crn"
GRAPHICS.ribbonWorm=yes
set field a_A/ Bfactor(a_/A )/3. name="_WORMRADIUS_"
display ribbon

Default: no

1. = "X-rocking"
2. = "Y-rocking"
3. = "Xy-rocking"
4. = "xY-rocking" <-- current choice
5. = "X-rotation"
6. = "Y-rotation"

real value of rocking range.

Default: 1.

GRAPHICS.rockingSpeed

real value of rocking or rotation speed.

Default: 1.

GRAPHICS.selectionLevel

preference for the selection level of as_graph selection. The atoms, residues, molecules or objects selected interactively in the graphics window are automatically stored in the as_graph variable. The preference may have the following values.

 
  GRAPHICS.selectionLevel = "atom" 
        1 = "object" 
        2 = "molecule" 
        3 = "residue" 
        4 = "atom" # default 
        5 = "variable" 

 
 GRAPHICS.selectionLevel = 3 

 
  GRAPHICS.selectionStyle = "color" 
        1 = "none"              
        2 = "cross" # the default choice 
        3 = "color"  
        4 = "both" 

1. "up-and-down"
2. "line interleaved" # current choice
3. "in-a-window"
4. "Sharp"
5. "Anaglyph"

The "Sharp" option is for SHARP manufactured 3D screens.

The "Anaglyph" option is for the stereoscopic 3D effect achieved by means of encoding each eye's image using filters of different (usually chromatically opposite) colors, typically red and cyan. The Anaglyph option is the easiest to used with inexpensive 3D glasses and and without any expensive 3D compatible hardware or monitors.

GRAPHICS.stickRadius

radius (in Angstroms) of a cylinder displayed as a part of stick or xstick graphical representation of a molecule.
Individual (residue-wide) control of stick radii.
In order to modify the default values of the radii from the command line use the set xstick r_newradius command For example:

 
set xstick a_/13:15 0.5

GRAPHICS.surfaceDotSize

Determines the size of the dot on the solvent accessible graphical surface area . This surface is controlled by the GRAPHICS.surfaceProbeRadius radius. If this parameter is changed, use

display surface refresh 

GRAPHICS.surfaceDotDensity

Determines the number of dots per square Angstrom on the graphical solvent accessible surface area . Do not confuse this parameter with surfaceAccuracy . The latter controls the surface and energy calculation and does not affect the displayed surface.

See also: GRAPHICS.surfaceProbeRadius and GRAPHICS.surfaceDotSize. Default (10).

GRAPHICS.surfaceProbeRadius

An increment to the van der Waals radii of atoms at thich the dotted atomic surface is calculated. It is used by the display surface command to display dotted van der Waals surface. If the GRAPHICS.surfaceProbeRadius is set to 1.4 the surface becomes equivalent to the solvent accessible surface with a probe of 1.4A (e.g. in show surface area ) .

Note, that in contrast to GRAPHICS.surfaceProbeRadius, the vwExpand parameter is used for calculations of the solved accessible areas (e.g. show surface area ).

Default (0.1)

Two parameters regulating the transparency of grobs.

• GRAPHICS.transparency[1] contains a value from 0. to 1. representing the level of transparency (0. solid, 0.99 - invisible)
• GRAPHICS.transparency[2] contains the brightness of the transparent surface from 0. to 1.

GRAPHICS.wormRadius

radius of coiled segments (i.e. those where the secondary structure is marked as "_") of a polypeptide chain in ribbon representation.

Warning: this parameter behaves as independent only in the GRAPHICS.ribbonWorm is yes . Otherwise, in case of a mixed ribbon representation display, ICM will reset the radius to the product of GRAPHICS.ribbonWidth and GRAPHICS.ribbonRatio in order to match thickness of the ribbon and the connecting coil. To make a variable worm radius of the cylinder set the residue field with a name "_WORMRADIUS_" Example:

read pdb "1crn"
GRAPHICS.ribbonWorm = yes
display ribbon  # uniform radius
set field a_A/ Bfactor(a_A/  )/3. name="_WORMRADIUS_"
display ribbon  # variable radius

Default (0.3).

[ GRID.gcghExteriorPenalty | GRID.margin | GRID.maxEl | GRID.minEl | GRID.maxVw | GRID.gpGaussianRadius ]

1. = "repulsive" <- the default
2. = "zero"

See also: gcMethod , GRID.margin

GRID.margin

real parameter determining the extra penalty-free space around the map bounding box if GRID.gcghExteriorPenalty = "repulsive" (see above). For any atom which gets outside the map-bounding box expanded by GRID.margin, its grid van der Waals energy ( "gc" or "gh" ) is penalized by the GRID.maxVw value. This is the same penalty value which atoms get if they severely clash with other atoms.

Therefore, if you set up grid energy calculations it is essential either to create a big enough box or set a sufficient margin to allow ligand rearrangements near the receptor surface. If GRID.margin is very large, your ligand will be "on the loose" and may spend too much time flying in open air. It is recommended that the margin is not larger than the diameter of your ligand.
Default: 0.00 A

See also: GRID.gcghExteriorPenalty , GRID.maxVw

GRID.gpGaussianRadius

The radius of the density Gaussian used to generate the property maps. Default: 1.2 A. See also:

• term "gp"
• set type property I_atomTypes R_upToSevenWeights
• make map potential "gp"

[ GROB.atomSphereRadius | GROB.relArrowSize | GROB.arrowRadius | GROB.relArrowHead | GROB.contourSigmaIncrement ]

GROB.relArrowSize

a real relative arrow size ([0.,1.]). Default: 0.2.

See also: makeAxisArrow , GROB.relArrowHead and GROB.`relArrowSize . Default: 0.5.

GROB.contourSigmaIncrement

a real increment in the sigma level used to re-contour an electron density map using the make grob m_eds add r_increment command.

This parameter is used in the GUI when plus and minus are pressed.

Default (0.1)

GUI

[ GUI.autoSave | GUI.autoSaveInterval | GUI.defaultLayoutAction | GUI.displayNDValueStyle | GUI.tableRowMarkColors | GUI.windowLayout | GUI.workspaceStyle | GUI.workspaceTabStyle | GUI.workspaceFolderStyle ]

To read about generating dialogs and menus from ICM see gui .

GUI.autoSave

a logical to activate the saving of the content of the session every GUI.autoSaveInterval seconds. If the program exists unexpectedly or crashes the session then can be restored.

GUI.autoSaveInterval

The number of seconds the session will save itself into a backup file as a precautionary measure against an unexpected termination or crash (see GUI.autoSave ) .

GUI.defaultLayoutAction

The behavior of ICM windows upon clicking the "Default Layout" button (third at the left bottom corner). The "Main" location is the upper right window that gets maximized upon pressing the fourth button.

  GUI.defaultLayoutAction = "3D to Main"
        1 = "3D to Main" <-- current choice
        2 = "Tables to Main"
        3 = "Alignmnets to Main"
        4 = "Html To Main"
        5 = "Keep Main"

GUI.displayNDValueStyle

The display of 'not-defined' values in rarray . Preference "empty" will leave the cell empty. The default will show letters ND .

  GUI.displayNDValueStyle = "text"
        1 = "text" <-- current choice
        2 = "empty"

Example: GUI.displayNDValueStyle = "empty"

GUI.tableRowMarkColors

E.g.

GUI.tableRowMarkColors = "#ff4444/#ffbb44/#44ff44/#4499ff/#ff44ff"

GUI.windowLayout

defines one of the two alternative ICM-panel layout styles:

1. = "traditional"
2. = "widescreen"

GUI.workspaceStyle

defines the look for objects and molecules in the ICM workspace panel.

1. = "all"
2. = "simple"

GUI.workspaceTabStyle

allows one to change the style of ICM-object tabs created in the workspace panel of ICM GUI.

1. = "icon title" # default
2. = "icon"
3. = "title"

GUI.workspaceFolderStyle

defines how many hierarchical levels of 3D molecular objects are shown in the Workspace panel.

1. = "closed"
2. = "object"
3. = "molecule" <-- current choice
4. = "residue"

[ IMAGE.quality | IMAGE.printerDPI | IMAGE.lineWidth | IMAGE.scale | IMAGE.stereoBase | IMAGE.stereoAngle | IMAGE.gammaCorrection | IMAGE.color | IMAGE.compress | IMAGE.generateAlpha | IMAGE.stereoText | IMAGE.previewer | IMAGE.previewResolution | IMAGE.lineWidth2D | IMAGE.bondLength2D | IMAGE.font | IMAGE.orientation | IMAGE.paperSize | IMAGE.rgb2bw | IMAGE.writeScale ]

• write image,
• write postscript,
• display trajectory image.

logical to toggle generation of the alpha (opacity) channel for the SGI rgb, tif and png image files to make the pixels of the background color transparent.
Be careful. The alpha channel is set to 1. for every pixel in your image which has the same color as the background. Therefore there is a danger that the same color will be accidentally used inside your image. If you nevertheless want to generate the alpha-channel, use a rare color your background (not black, but rather green, e.g. rgb = {0.,0.976,0.} .
Default: yes

• 10 - very rough ( 1/10th of an inch )
• 20 - a reasonable preview but no fine details
• 30 - a fine preview, do not increase it any higher since the file will become too large.

IMAGE.lineWidth2D

the default integer thickness of bonds in chemical 2D drawing that is preserved upon the Copy Image command. This is useful for adjusting the table display and cutting and pasting from ICM to external documents.

See also: write image chemical , IMAGE.font

Default: 1.5 pixels

IMAGE.bondLength2D

real length of a chemical bond (in inches) in chemical 2D drawings upon the Copy Image command. To make your molecule large, increase it. This is useful for cutting and pasting from ICM to external documents. Default (0.4 inches)

IMAGE.font

This string defines the font used for elements in a chemical drawing. Default ( "15px Arial" )

IMAGE.orientation

preference to specify image orientation.

1. = "portrait" <- default
2. = "landscape"
3. = "auto"

1. = "Letter (8.5x11")" <- default
2. = "Legal (8.5x14")"
3. = "11x17""
4. = "A4 (210x297mm)"
5. = "A3 (297x420mm)"

 
  write image png window= N * View(window)  

[ LIBRARY.men | LIBRARY.res ]

 
 LIBRARY.bbt="icm"  # bond bending types 
 LIBRARY.bci="icm"  # mmff bond charge increments 
 LIBRARY.bst="icm"  # bond stretching types 
 LIBRARY.clr="icm"  # colors, gui controls 
 LIBRARY.cmp="icm"  # amino-acid comparison matrix 
 LIBRARY.cnt="icm"  # distant restraint types 
 LIBRARY.cod="icm"  # atom codes 
 LIBRARY.hbt="icm"  # hydrogen bonding types 
 LIBRARY.hdt="icm"  # hydration types 
 LIBRARY.lps="icm.lps"  # loop database, rebuilt with write model [append] 
 LIBRARY.men="icm.gui"  # GUI commands. can be reloaded with 'read gui'
 LIBRARY.mmbbt= "mmff"  # mmff bond bending 
 LIBRARY.mmbst= "mmff"  # mmff bond stretching 
 LIBRARY.mmtot= "mmff"  # mmff torsions 
 LIBRARY.mmvwt= "mmff"  # mmff van der Waals 
 LIBRARY.rst="icm"  # variable restraint types 
 LIBRARY.tor="icm"  # precomputed icmff torsion params 
 LIBRARY.tot="icm"  # torsion types 
 LIBRARY.vwt="icm"  # van der Waals types 
 LIBRARY.res={"icm","usr"} 

 
 LIBRARY.res=LIBRARY.res // "./benz.res" # just append 
 LIBRARY.cod="./newCodes.cod" 
 read library 

LIBRARY.men

LIBRARY.men defines a string with a filename to the file with the menus.

Two possibilities:

• define LIBRARY.men in the _startup file for the desired menus to be activated
• The menus can later be extended with the read gui filename command.

# open the $ICMHOME/_startup file and add this line
  LIBRARY.men = Getenv("HOME")+"/.icm/icm.gui"  # now the ICM GUI will invoke your file 

LIBRARY.res

a string array or file names of the residue libraries . File extensions can be omitted, e.g. LIBRARY.res={"icm","user","./lib/mylibrary"}

OBJECT

Controls atom requisites which are written to a file in the write object command. Extensions are automatically added. Defaults:

 
 OBJECT.bfactor  =yes 
 OBJECT.charge   =yes 
 OBJECT.occupancy=yes 
 OBJECT.site     =yes 
 OBJECT.display  =no 
 OBJECT.library  =no 
 OBJECT.auto     =no 

 
 OBJECT.auto = no 
 OBJECT.display = yes 
 read object "crn" 
 display ribbon a_/1:40 
 set plane 2  
 display cpk a_/12 
 write object "tm"  # graphics and planes are written 
 delete a_*. 
 read object "tm"    

[ PLOT.box | PLOT.color | PLOT.font | PLOT.fontSize | PLOT.gridLineWidth | PLOT.lineWidth | PLOT.markSize | PLOT.numberOffset | PLOT.Yratio | PLOT.logo | PLOT.orientation | PLOT.seriesLabels | PLOT.labelFont | PLOT.rainbowStyle | SEQUENCE.restoreOrigNames ]

PLOT.box

rarray of the origin and relative sizes of the ICM plot frame: { X_origin, Y_origin, X_size, Y_size }. Box {0. 0. 1. 1.} fits the page optimally.
Default ({0. 0. 1. 1.}).

PLOT.font

preference for the title/legend font. The font size can only be redefined by editing the *.eps file (search for the number before the scalefont string). Available choices:

• 1 = "Times-Bold"
• 2 = "Times-Roman" <- default choice
• 3 = "Helvetica"
• 4 = "Courier"
• 5 = "Symbol"

PLOT.gridLineWidth

real width of grid lines. Use a small number (e.g. 0.01 for thin grid lines). Default (0.2).

PLOT.numberOffset

integer offset for the X-coordinate with the number option. This option is used in a number of macros generating multi-section plots for amino-acid sequences.
Default (0).

• 1 = "none"
• 2 = "right" <- default choice
• 3 = "left"
• 4 = "top"
• 5 = "bottom"

• 1 = "Times-Bold"
• 2 = "Times-Roman" <- default choice
• 3 = "Helvetica"
• 4 = "Courier"
• 5 = "Symbol"

• 1 = "black/white"
• 2 = "blue/white/red" <- default choice
• 3 = "blue/rainbow/red"

 
 read matrix  # def.mat is the default one 
 PLOT.rainbowStyle=1   
 plot area def display   # grey-scale, automatic min and max 
 PLOT.rainbowStyle=3   
 plot area def color={-10.,0.} display  # enforce new range 
 PLOT.rainbowStyle=2   
 plot area def transparent={-2.,8.} display  
# low values - blue, middle [-2.,8.] - invisible, large red 

When sequences from GenBank are read in ICM, they get a comment (or description) line that describes their original complicated name. The description gets this : " Orig.name: "origSeqName. This name can be restored upon writing in various formats including write alignment fasta if this flag is set to yes . By default this logical variable is set to no . Example:

delete a,b,c
make sequence 3 10 # creates sequences a b c
set comment a "an experimental sequence Orig.name: expr "
align a b c  # creates aln
write aln fasta "tmp" # keeps a b c, default should be no, unless you redefined it
write aln fasta "tmp" SEQUENCE.restoreOrigNames=yes  # restores the names.

SITE

[ SITE.appendStyle | SITE.defSelect | SITE.labelOffset | SITE.labelStyle | SITE.labelWrap | SITE.showSeqSkip | SITE.wrapComment ]

SITE.appendStyle =

1. "none"
2. "merge source"

Allows to extend the site description with the name of a new sequence, even if the text of the description if the same in the copy site command. For example, if there is a site in two different sequences, say A_PIG A_DUCK, but they are being transferred to a third sequence with two consecutive copy site commands, the resulting description may indicate something like that:

• FT 135 135 ACT_SITE active site Serine (from A_PIG), if the style is 1
• FT 135 135 ACT_SITE active site Serine (from A_PIG,A_DUCK), if the style is 2

See also:

• site
• copy site

SITE.defSelect

string of significant site types (shown as one letter abbreviations) Sequence identity in the alignment positions which have one of those sites is additionally rewarded in the alignment score calculation.
Default: "ABFGLMstepm"

SITE.labelOffset

(default 5. A) the real offset of the site label with respect to the residue label atom.

SITE.labelStyle

the style preference of the displayed site information:

1. "none"
2. "symbol" # one letter symbol, see site .
3. "comment"
4. "full"

SITE.wrapComment

the integer length of the comment line. The longer lines will be automatically wrapped in the graphics view. Default: 30

TOOLS

[ TOOLS.edsDir | TOOLS.membrane | TOOLS.minSphereCubeSize | TOOLS.pdbChargeNterm | TOOLS.pdbReadNmrModels | TOOLS.rebelPatchSize | TOOLS.smilesXyzSeparator | TOOLS.superimposeMaxIterations | TOOLS.superimposeMinAtomFraction | TOOLS.superimposeMaxDeviation | TOOLS.tsToleranceRadius | TOOLS.tsShape | TOOLS.tsWeight | TOOLS.writePdbRenameRes ]

parameters for some ICM tools. The TOOLS.superimpose.. parameters control the superimpose minimize

TOOLS.edsDir

A directory for the electron density map repository. If this path is empty (i.e. TOOLS.edsDir=="" ) the loaded maps from are cashed into s_userDir + "/data/eds/" directory

See loadEDS and loadEDSweb

TOOLS.membrane

This real array contains the geometrical parameters defining shapes with lipids or water for implicit solvation calculations. The array may contain multiple sections of 5 elements each.
Each atom is considered either buried by other explicit atoms of the objects or exposed. Five types of environment are possible depending on the surfaceMethod and the "sf" term, with the first one (the 'membrane') being suitable for the membrane modeling

• "membrane" ( surfaceMethod=4;set term "sf", exposed atom solvation density in col3 or col7 )
• constant tension ( surfaceMethod=2; set term "sf"; surfaceTension=0.02 )
• water ( surfaceMethod=2;set term "sf", exposed atom solvation density in col3 of icm.hdt )
• apolar ( surfaceMethod=3;set term "sf", exposed atom solvation density in col4 icm.hdt )
• vacuum ( set term "sf" off )

If the surfaceMethod is defined as "membrane" and term "sf" is on, then each atom can be either in water environment or in lipid environment. The attribution is done according to the atom coordinates and a series of shapes coded by the TOOLS.membrane array.

Each shape is coded by 5 numbers in the TOOLS.membrane array. The following shapes with lipid-like environment can be introduced.

Name	Type(e1)	e2	e3	e4	e5	Description	Examples
membrane	1	z_bott	z_top	z_bmargin	z_tmargin	Z-membrane with transitional layers	{1.,0.,30.,5.,5.}
z-chimney	2	x1	y1	x2	y2	infinite rectangular beam in Z direction	{2.,-5.,-5.,5.,5.}
z-cylinder	3	xct	yct	radius	0.	infinite round cylinder in Z direction	{3.,7.,7.,15.,0.}
cube	4	xct	yct	zct	half-edge-length	cube with defined center and half-size	{4.,0.,0.,0.,10.}
sphere	5	xct	yct	zct	radius	sphere with defined center and radius	{5.,0.,0.,0.,10.}

Each shape only defines the environment inside itself and is applied sequentially. To define water environment inside preceding lipid shape, use the negative type, e.g. {..lipid_shape.., -4.,0.,0.,0.,3.} for a water cube of half size 3.. Examples:

TOOLS.membrane = {1.,0.,30.,5.,5.} # one membrane from z=0 to z=30A with 5A transitional layers
TOOLS.membrane = {5.,0.,0.,0.,4.,  5.,10.,10.,10.,4.} # two lipid spheres at 0,0,0 and 10,10,10
TOOLS.membrane = {5.,0.,0.,0.,6., -5.,0.,0.,0.,3.}    # a spherical layer, two concentric spheres

Example:

TOOLS.membrane = {1.,0.,30.,5.,5.}
set terms only "vw,14,hb,el,to,ss,ts,sf"  # sf is on
build string IcmSequence( "EACARVAAACEAAARQ" "nh3+" "coo-" )
set a_/A String("H",Nof(a_/A))  # make a helix
translate a_ {0. 0. 0.}
display xstick
display box {0. 0. 0. 50. 50. 30.}  # purple box for visualization
display origin
connect  a_   # position it roughly in the membrane
set selftether a_/8/ca {0. 0. 20.}  # to prevent it from flying away
TOOLS.tsToleranceRadius = 15.
montecarlo v_//V  # rigid placement
#
montecarlo v_//V,xi*  # flexible placement

See also: icm.hdt , surfaceMethod = 4 , energy term "sf"

TOOLS.minSphereCubeSize ( default = 5.)

This parameter adjusts the minimal size of a cube for fast scanning of interatomic pairs. These calculation may be necessary when pairs of atoms are processes during an energy calculation or in a Sphere function. If an odd atom or group of atoms is far away from the rest of the object (an unusual and undesired situation), an exceedingly large number of cubes between the groups need to be created. In this case the minimal size of an edge needs to be increased to deal with those sparse atoms. If you see a warning involving this parameter, have a look at the coordinates of your object and make sure that the atom positions are correct.

TOOLS.pdbChargeNterm

TOOLS.pdbChargeNterm logical to automatically charge the N-terminal residue in read pdb command if it matches the first residue in construct sequence in _SEQRES_ field of a PDB file.

Example:

read pdb "1crn" TOOLS.pdbChargeNterm = yes
convertObject a_ yes no no no yes no yes ""

See also read pdb

TOOLS.pdbReadNmrModels

TOOLS.pdbReadNmrModels = "first"

1. = "first" : reads only one model from a multi-model (e.g. NMR) pdb file
2. = "all" : reads all models from a multi-model (e.g. NMR) pdb file and creates a separate object for each of them
3. = "all stack" : creates one object and loads all other models as a stored cartesian stack

This preference is set to "first" by default. Resetting it to "all"is equivalent to option all in read pdb . Setting the preference to 3 is equivalent to the read pdb all stack s_pdbMultiModelFile command. Example:

TOOLS.pdbReadNmrModels = "all"
read pdb "1dkc"  # all 10 models are read in as a_1dkc_1., .., a_1dkc_10. 
read pdb "1dkc" TOOLS.pdbReadNmrModels=3 # one object with a built-in stack is created

TOOLS.rebelPatchSize

Defines resolution of the electrostatic coloring. Smaller values will lead to slower calculation but better results. You may try a range from 0.3 for relatively small proteins to 2. for very large ones.

Default: 1.

TOOLS.smilesXyzSeparator

ICM has an option to generate smiles with coordinates which is a much more compact (and one line only) replacement for an mol / .sdf file

TOOLS.superimposeMaxIterations

The maximal number of iterative superpositions with gradually improved weights in the superimpose minimize procedure that optimizes the weighted rmsd to find the best superposition core. Do not afraid to set this number to a very large one since the procedure will exit earlier if the convergence is achieved.

Default: 10

TOOLS.superimposeMinAtomFraction

The minimal fraction of equivalent atom pairs that will be superimposed with significant weights in the superimpose minimize procedure.

Default: 0.5

TOOLS.superimposeMaxDeviation

Determines the maximal atom deviation for determining the core subset of atoms for which the unweighted RMSD is reported in r_2out in the superimpose minimize procedure. The unweighted rmsd for a subset must be lower than this parameter.

Default: 2.0

TOOLS.tsToleranceRadius

radius around atoms where the deviations from the target are not penalized

Default: (0.)

See also: selftether , term ts , TOOLS.tsShape

TOOLS.tsShape and TOOLS.tsShapeData

This preference and a rarray of parameters supports positional restraints for all non-virtual atoms of the current object. It can be used concurrently with atom-specific selftethers and does not need the set selftether as command. Some selftethers can have individual status "box" (see set selftether ), these atoms are controled by that status and not TOOLS.tsShape preference. The TOOLS.tsShape preference has the following values:

  1 = "none" <-- current choice
  2 = "sphere"  # also a spherical layer if two radii are specified
  3 = "box"

The TOOLS.tsShapeData real array contains the parameters needed for a shape restraint. Note that while TOOLS.tsShape preference can be specified as an inline argument of a minimize or montecarlo command, the array can not. Therefore the values need to be filled before you call the command, e.g.

TOOLS.tsShapeData = {20.}  # radius of the sphere
minimize "vw,ts" TOOLS.tsShape=2 

sphere.For the sphere option the radii and the center x,y,z parameters can be specified.

TOOLS.tsShapeData = { [ minimal_radius ] max_radius [ x y z ] }

The radii can be provided in any order. The default radius is 20. and the center of the spherical restraint is the origin ( {0. 0. 0.}

Examples:

 TOOLS.tsShapeData = {10.} # keep atoms inside R=10
 TOOLS.tsShapeData = {10. 10.} # keep atoms on the surface of the sphere R=10
 TOOLS.tsShapeData = {10. 15.} # penalty free is the spherical layer between R=10 and 15
 TOOLS.tsShapeData = {10. 15. 3. 3. 3.} # layer between R=10 and 15 around  3.//3.//3. center
 TOOLS.tsShapeData = {10.}//Mean(Xyz(a_//!vt*)) # do not let molecule fly beyond 10A from where it is now 

box.

TOOLS.tsShapeData = {x_min ,y_min ,z_min ,x_max ,y_max ,z_max }

These six parameters are compatible with the Box function. Example:

TOOLS.tsShapeData = Box( a_// 3. ) 
#
TOOLS.tsShapeData = 100.//100.//-1.//100.//100.//1.  # keep atoms in 1A layer around Z-plane

individual atoms in a boxNote that a box defined by TOOLS.tsShapeData (need six numbers) can also be used by individual atoms set to interact with a box with the following command:

set selftether "box" as_sel 

See also: selftether , term ts

TOOLS.tsWeight

Weight for a special terms "ts" that can be used in minimize to tether the atoms to its initial set of coordinates (see selftether ). To keep only some atoms self-tethered, use option selftether= as_selfTetheredAtoms of the minimize command. The convert command and set selftether set them.

Example:

  build string "lys"
  randomize v_//x*
  minimize "vw,to,ts"  selftether=a_//ca,c,n  TOOLS.tsWeight=10.  

Default: (0.)

See also: term ts , selftether , TOOLS.tsShape.

TOOLS.writePdbRenameRes

Defines translation rules for the internal ICM residue names in show pdb or write pdb commands. For example, names ra for adenosine, or cyss for the bonded cysteins, can be translated to other names during the pdb export into ade or cyx . The format is the following: icm_res_name , exported_pdb_res_name ; ... , e.g.

 TOOLS.writePdbRenameRes = "cyss,cyx;his,hid"  # will rename two residues

WEBLINK

This table contains definitions of types of web links used in the web, show html, and write html commands. The table is read from "WEBLINK.tab" file from the $ICMHOME directory. Change this file for your own definitions. The weblink specification is used to extend the argument string substituted for %s (e.g. "IL2_HUMAN" element of the table array linked according to the type
SP %s "http://www.aaa?%s" will be transformed into the <a href="http://www.aaa?IL2_HUMAN">IL2_HUMAN</a> link. If %Ns specification is used, only N characters of the argument string will be retain in the link. For example,
PDB %s "http://www.pdb?%4s" and 1xyz_a15_25 (specifying chain and residue range) will be translated into
<a href="http://www.pdb?1xyz">1xyz</a>_a15_25 which in your browser will look like this: 1xyz_a15_25
"AUTO" is another type which can be used in the link S_ "TYPE" ... expression. In this case the DB type is automatically recognized according the database reference string pattern (see also WEBAUTOLINK). An example table:

 
#>T WEBLINK 
#>-DB------DR--LINK------- 
 PDB     %s  http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=pdb|%4s|&Dopt=g 
 NCBI    g%s http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=%s&Dopt=g 
 EMBL    %s  http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=emb|%s|&Dopt=g 
 SP      %s  http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=sp||%s&Dopt=g 
 SPA     %s  http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=sp|%s|&Dopt=g 
 PROSITE %s  http://saturn.med.nyu.edu/srs/srsc?[PROSITE-acc:%s] 
 MED     %s  http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&uid=%s&dopt=r 

 
 read table "seqcomp.tab"  #contains references to different databases 
 web SR link SR.NA1 "PDB" SR.NA2 "AUTO"   

 
 read table "seqcomp.tab"  #contains references to different databases 
 web SR link SR.NA1 "AUTO" SR.NA2 "AUTO"