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[ CONSENSUS | CONSENSUSCOLOR | FILTER | FTP | GRAPHICS | GRID | GROB | GUI | IMAGE | LIBRARY | OBJECT | PLOT | SITE | TOOLS | WEBLINK | WEBAUTOLINK ]
The following predefined icm-shell tables are collections of different icm shell objects related to a certain topic. Note that these tables (as opposed to user-defined ICM tables ) usually only have the header section. You can show and list them. You can also change any table element by the usual icm assignment:IMAGE.color = yes # this member is a logical IMAGE.stereoBase = 2.5 # redefine real distance between stereo panels
CONSENSUS |
#>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 -
CONSENSUSCOLOR |
#>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 |
[ FILTER.Z | FILTER.gz | FILTER.uue ]
contains filters which can be applied to the input stream in the read command. Components have names corresponding to standard file name extensions; their string value is a unix filter. Token %s is a placeholder for the file name. The provided defaults can be redefined in your _startup file. You can also add your own extensions and filters by doing the following:z = "pcat %s" # define the action for the unix packed files group table append FILTER header z # append new filter to the structureThe mechanism ICM employs allows to keep the transformed files intact and avoid creating temporary files when possible (e.g. uuencode unix command always creates an output file). Existing extensions and defaults are given below. You may need to redefine the defaults by adding the exact path to the utility or using alternatives.
FILTER.Z |
FILTER.gz |
FILTER.uue |
"sed 's:begin .*:begin 600 /tmp/UUPtm:' %s | uudecode && cat /tmp/UUPtm && rm -f /tmp/UUPtm"This works for UNIX file system, write your own on the PC, if needed.
FTP |
[ FTP.createFile | FTP.keepFile | FTP.proxy | HTTP.proxy ]
table which controls reading from ftp.FTP.createFile |
FTP.keepFile |
FTP.proxy |
String format: ftp.proxy.host.com[:port]
HTTP.proxy |
String format: [user[:pass]@]http.proxy.host.com[:port]
GRAPHICS |
[ GRAPHICS.atomLabelShift | GRAPHICS.atomValueCircles | GRAPHICS.ballRadius | GRAPHICS.ballStickRatio | GRAPHICS.clashWidth | GRAPHICS.chainBreakStyle | GRAPHICS.chainBreakLabelDisplay | GRAPHICS.cpkClipCaps | GRAPHICS.displayLineLabels | GRAPHICS.displayMapBox | GRAPHICS.dnaBallRadius | GRAPHICS.dnaRibbonRatio | GRAPHICS.dnaRibbonWidth | GRAPHICS.dnaRibbonWorm | GRAPHICS.dnaStickRadius | GRAPHICS.formalChargeDisplay | 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.resLabelShift | GRAPHICS.ribbonCylinderRadius | 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 ]
display parameters for different graphics representations.
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.resLabelShift Default (0)
GRAPHICS.atomValueCircles |
GRAPHICS.atomValueCircles allows to display a circle with a positive value on every atom for those atom fields:
The radius of the circle and the value tranformation upon changing hydrogen display is defined as follows:
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 |
GRAPHICS.ballStickRatio |
GRAPHICS.clashWidth |
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:
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 |
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.
See also: GRAPHICS.chainBreakStyle
GRAPHICS.cpkClipCaps |
preferences to control the way the cpk spheres are being displayed when cut by a clipping plane.
Both capping methods have some side effects and slow down the graphics performance. User discretion is advised.
See also:
GRAPHICS.displayLineLabels |
GRAPHICS.displayMapBox |
GRAPHICS.dnaBallRadius |
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.dnaRibbonRatio |
GRAPHICS.dnaRibbonWidth |
GRAPHICS.dnaRibbonWorm |
GRAPHICS.dnaStickRadius |
GRAPHICS.formalChargeDislplay |
a preference regulating the formal charge visualization of the visible atoms:
See also:
GRAPHICS.grobLineWidth |
GRAPHICS.hbondStyle |
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> angleThe best possible value for a non-linearity angle is 0. . The display dialog has a small button to roll through this preference. See also: GRAPHICS.hbondWidth .
GRAPHICS.hbondRebuild |
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.
See also:
GRAPHICS.hbondMinStrength |
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:
GRAPHICS.hbondWidth |
GRAPHICS.sketchAccents |
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.hetatmZoom |
GRAPHICS.hydrogenDisplay |
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
GRAPHICS.light |
Elements Property Range Default Comment |
---|
GRAPHICS.light[1] shininess 0.,1. 1. property of the solid material |
GRAPHICS.light[2:4] ambient light 0.,1. {0.15 0.15 0.15} intensity of RGB for ambient light |
GRAPHICS.light[5:7] diffuse light 0.,1. {0.6 0.6 0.6} intensity of RGB for diffuse light |
GRAPHICS.light[8:10] specular light 0.,1. {0.35 0.35 0.35} intensity of RGB for specular light |
GRAPHICS.light[11:13] emission 0.,1. {0. 0. 0.} intensity of RGB for emitted light |
display new reflectioncommand.
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.}See also: GRAPHICS.light .
GRAPHICS.mapLineWidth |
GRAPHICS.occupancyDisplay |
A silly example.
GRAPHICS.occupancyDisplay="label" build string "se ala his" set occupancy a_//n* 0.5 display xstick
See also:
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.quality |
GRAPHICS.quality = 15 display ribbon # press Ctrl-D for the fog effect, move clipping planes, change fogStart write image png window=2*View(window)
GRAPHICS.rainbowBarStyle |
GRAPHICS.resLabelDrag |
GRAPHICS.resLabelShift |
a non-negative integer number of spaces preceding a residue label. 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. See also:
GRAPHICS.ribbonRatio |
GRAPHICS.ribbonWidth |
GRAPHICS.ribbonWorm |
Default: no
GRAPHICS.rocking |
GRAPHICS.rockingRange |
real value of rocking range.
Default: 1.
GRAPHICS.rockingSpeed |
Default: 1.
GRAPHICS.selectionLevel |
GRAPHICS.selectionLevel = "atom" 1 = "object" 2 = "molecule" 3 = "residue" 4 = "atom" # default 5 = "variable"
GRAPHICS.selectionLevel = 3or from GUI by selecting the level combo box with the following choices: O (object), M (molecule), R (residue), x (atom), or an icon of a torsion (variable).
GRAPHICS.selectionStyle |
GRAPHICS.selectionStyle = "color" 1 = "none" 2 = "cross" # the default choice 3 = "color" 4 = "both"In the 1-st mode ( "none") only a single selection mark is shown. It is convenient when you do not want multiple selection marks to overwhelm the image. The 3-rd mode is incovenient if you want to try different colored displays for the selected fragments.
GRAPHICS.stereoMode |
GRAPHICS.stickRadius |
set xstick a_/13:15 0.5In this case the ball radius will be changed according to the radio of the default parameters (e.g. GRAPHICS.ballRaduis/GRAPHICS.stickRadius )
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 refreshto update the dot size.
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)
GRAPHICS.transparency |
Two parameters regulating the transparency of grobs.
GRAPHICS.wormRadius |
GRID |
[ GRID.gcghExteriorPenalty | GRID.margin | GRID.maxEl | GRID.minEl | GRID.maxVw | GRID.gpGaussianRadius ]
parameters for the grid energy calculations (see also "gh,gc,ge,gs,sf" energy terms).GRID.gcghExteriorPenalty |
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. |
GRID.maxEl |
GRID.minEl |
GRID.maxVw |
GRID.gpGaussianRadius |
The radius of the density Gaussian used to generate the property maps. Default: 1.2 A. See also:
GROB |
[ GROB.atomSphereRadius | GROB.relArrowSize | GROB.arrowRadius | GROB.relArrowHead | GROB.contourSigmaIncrement ]
Parameters related to graphics objects. See also the Grob family of functions.GROB.atomSphereRadius |
GROB.relArrowSize |
GROB.arrowRadius |
See also: makeAxisArrow , GROB.relArrowHead and GROB.`relArrowSize . Default: 0.5.
GROB.relArrowHead |
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.tableRowMarkColors | GUI.windowLayout | GUI.workspaceStyle | GUI.workspaceTabStyle | GUI.workspaceFolderStyle ]
This parameter table contains some settings for the GUI (see below). Most of the settings are stored automatically in the s_userDir + "/config/icm.cfg" fileTo 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.tableRowMarkColors |
E.g.
GUI.tableRowMarkColors = "#ff4444/#ffbb44/#44ff44/#4499ff/#ff44ff"
GUI.windowLayout |
defines one of the two alternative ICM-panel layout styles:
GUI.workspaceStyle |
defines the look for objects and molecules in the ICM workspace panel.
GUI.workspaceTabStyle |
GUI.workspaceFolderStyle |
IMAGE |
[ 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.orientation | IMAGE.paperSize | IMAGE.rgb2bw | IMAGE.writeScale ]
table contains settings used by the following commands creating image files:IMAGE.quality |
IMAGE.printerDPI |
IMAGE.lineWidth |
IMAGE.scale |
IMAGE.stereoBase |
IMAGE.stereoAngle |
IMAGE.gammaCorrection |
IMAGE.color |
IMAGE.compress |
IMAGE.generateAlpha |
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
IMAGE.stereoText |
IMAGE.previewer |
IMAGE.previewResolution |
IMAGE.lineWidth2D |
integer thickness of bonds in chemical 2D drawing upon the Copy Image command. This is useful for cutting and pasting from ICM to external documents. 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.orientation |
IMAGE.paperSize |
IMAGE.rgb2bw |
IMAGE.writeScale |
write image png window= N * View(window)command where N defines if the image is N-times bigger than the screen image. This parameter can be changed from File/Preferences/Image dialog.
LIBRARY |
[ LIBRARY.men | LIBRARY.res ]
table containing string paths of the icm parameter files, which are loaded by the read library [mmff] command. The library files will be taken from the s_icmhome directory if no explicit directory is provided. Extensions are automatically added. Defaults: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:
# 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 |
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 |
[ PLOT.numberOffset | PLOT.fontSize | PLOT.lineWidth | PLOT.markSize | PLOT.Yratio | PLOT.logo | PLOT.color | PLOT.orientation | PLOT.seriesLabels | PLOT.font | PLOT.labelFont | PLOT.rainbowStyle | PLOT.box | SEQUENCE.restoreOrigNames ]
Contains settings used by the plot command. All real sizes are expressed in the Postscript "points" equal to 1/72" ( about 1/3 mm ).PLOT.numberOffset |
PLOT.fontSize |
PLOT.lineWidth |
PLOT.markSize |
PLOT.Yratio |
PLOT.logo |
PLOT.color |
PLOT.orientation |
PLOT.seriesLabels |
PLOT.font |
PLOT.labelFont |
PLOT.rainbowStyle |
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
PLOT.box |
SEQUENCE.restoreOrigNames |
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 ]
This table contains parameters and preferences used to display the sites, or important residues.SITE.appendStyle |
SITE.appendStyle =
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:
See also:
SITE.defSelect |
SITE.labelOffset |
SITE.labelStyle |
SITE.labelWrap |
SITE.showSeqSkip |
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.pdbReadNmrModels | 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:
The surfaceMethod is defined as membrane 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
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.pdbReadNmrModels |
TOOLS.pdbReadNmrModels = "first"
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.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. 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 = {xmin ,ymin ,zmin ,xmax ,ymax ,zmax }
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
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 residuesSee also: show pdb write pdb .
WEBLINK |
#>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"
WEBAUTOLINK |
read table "seqcomp.tab" #contains references to different databases web SR link SR.NA1 "AUTO" SR.NA2 "AUTO"
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