[ 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

#>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]

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.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 ]

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 ..

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 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

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

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

• GRAPHICS.clipStatic

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:

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 = "complex shapes"

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

default radius of a dot/vertex in a grob.

See also: lineWidth , GRAPHICS.grobLineWidth

Default: 3.0.

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)

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

See also: GRAPHICS.hbondAngleSharpness Default: 1.

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

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

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.

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

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.}

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

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 = 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"

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 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

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.

Default: 1.

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.

set xstick a_/13:15 0.5

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

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).

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.

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

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.

See also: GRID.gcghExteriorPenalty , GRID.maxVw

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 ]

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

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.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 .

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.

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 ) .

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 = "text"
        1 = "text" <-- current choice
        2 = "empty"

Example: GUI.displayNDValueStyle = "empty"

E.g.

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

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

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

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

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

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

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.

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

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)

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

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 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

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

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 ]

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

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

• 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.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

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

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

[ 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

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

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.

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"

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

Example:

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

See also read pdb

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

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.

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

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

Default: 0.5

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

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

Default: (0.)

See also: selftether , term ts , TOOLS.tsShape

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

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.

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

#>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"