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RasMol v2.7.3Quick Reference Card

Copyright Roger Sayle 1992-1999V2.6x1 Mods Copyright Arne Mueller1998; ucb Mods Copyright

UC Regents/ModularCHEM 1995-1996; RasTop 1.3 Copyright Philippe Valadon 2000; V2.7.3 Copyright Herbert J. Bernstein1998-2005

Mouse ButtonsClicking on an atom identifies that atom in the command window. Movingthe mouse whilst holding mouse buttons and/or control keys manipulatesthe molecule. The default bindings are described below.

Mac Windows Action--- Left Rotate X-Y (or Z)Command Right Translate X-YShift Shift Left ZoomShift -Cmnd Shift Right Rotate ZControl Control Left Z-Clipping (Slab)

General Commands

load [format] Load a molecule (up to 5)pdb Brookhaven Protein Databankmdl Molecular Design Limited's Mol filemol2 Tripos' Sybyl Mol2 file formatalchemy Tripos' Alchemy file formatcharmm CHARMm format card filexyz MSC's XMOL XYZ file formatmopac J.P. Stewart's MOPAC file formatcif IUCr CIF or mmCIF file format

exit Exit from RasMol Scriptquit Terminate pgm execution

help [topic [subtopic]] Display on-line help topic

select Update part of moleculerestrict Display only part of mol.

set bondmode [mode] Change bond selection

script Execute file of commands

zap Delete molecule

Bond Commands

bond + Add a bondbond pick

Pick bond for rotationunbond Remove a bond

Display Commands

wireframe [boolean] Display wireframewireframe Display stick bondsset bondmode all Mark all atomsset bondmode none Mark no atomsset bondmode not bonded

Mark non-bonded atomsspacefill [boolean] Display spacefill spheresspacefill Specify atom sphere radiusspacefill temperature

spacefill userstar ... Display stars for spheressurface molecule surface solvent

Display molecule surfacebackbone [boolean] Display alpha backbonebackbone Specify backbone radius

ribbons [boolean] Display solid ribbonsribbons Specify ribbon widthstrands [boolean] Draw ribbon as strandsstrands Specify ribbon widthset strands Number of ribbon strands

label [boolean] Draw default atom labelslabel Label with arbitrary textset fontsize [FS|PS]

Set label font heightset fontstroke Set label stroke width

ssbonds [boolean] Display disulphide bondsssbonds Specify ssbond radiusset ssbonds backbone SSBonds between alphasset ssbonds sidechain SSBonds between sulphurshbonds [boolean] Display hydrogen bondshbonds Specify hbond radiusset hbonds backbone HBonds between alphasset hbonds sidechain HBonds donor/acceptor

dots [boolean] Display dot surfacedots Specify dot density

set solvent [boolean] VDW or solvent surfaceset radius Specify probe sphere rad.set axes [boolean] Display co-ordinate axesset boundbox [boolean]

Display bounding boxset unitcell [boolean] Display crystal unit cell

set monitor [boolean] Show distance monitor labelsset backfade [ boolean]

Shade to any background colorset display selected Currently selected portionset picking Series of 13 commands:

off | ident | distance| angle| torsion | label | monitor | centercoord | bond | atom | group | chain

Colour Commands

colour [object] Colour representation

Objects:atoms bonds backboneribbons labels hbondsssbonds dots axesribbons1 ribbons2

Predefined Colours:

Black Blue BlueTint BrownCyan Gold Grey GreenGreenBlue GreenTint HotPink MagentaOrange Pink PinkTint PurpleRed RedOrange SeaGreen SkyBlueViolet White Yellow YellowTon

t

Atom Colour Schemes:cpk, cpknew amino shapelygroup chain structuretemperature charge useralt model

colour hbonds type Colour hbonds by offsetcolour dots potential Display potential surface

Manipulation Commands

depth[boolean] Enable/disable back-clippingdepth Move back-clipping plane

molecule Specify molecule to manipulate

rotate [-] Rotate moleculerotate bond Rotate bondrotate molecule Rotate selected moleculerotate all Rotate all molecules

translate [-] Translate molecule

zoom [boolean] Scale moleculezoom Specify magnification

slab [boolean] Enable/disable slabbingslab Move Z-clipping plane

centre [expression] {centre|translate}Set centre of rotation

reset Initial transformation

set stereo [boolean] Control L&R images

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Scripted Commandsload [format] inline Load molecule

from scriptpause Suspend script executionecho Display text on

command linerefresh Redraw imageset write [boolean] Save & write in scripts

Atom ExpressionsPredefined Sets: alpha

hydrophobicResidue Ranges: 3,16,12

9-20Boolean Operators: backbone and not alpha

ligand or 196-199Primitive Expressions: cys, glu, arg, as?

ser70a, **p, glu24:1hem*p.fe, *.sg

Comparison Operators: atomno=4,atomno=6temperature>=900

Within Expressions: within(8.0,ligand)

Predefined Setsat acidic acyclic aliphaticalpha amino aromatic backbonebasic bonded buried cgcharged cyclic cystine helixhetero hydrogen hydrophobic ionslarge ligand medium neutralnucleic polar protein purinepyrimidine selected sheet sidechainsmall solvent surface turnwater

define User-defined sets

Rendering Commandsbackground Set background colourset ambient [value] Depth-cueing/lightingset shadows [boolean] Enable/disable shadowsset specular [boolean] Enable atom highlightsset specpower [value] Control atom 'shininess'set shadepower [value] Control atom 'contrast

Language CommandsEnglish English menus and messagesFrench French menus and messagesItalian Italian menus and messagesSpanish Spanish menus and messages

Export Commands

write [format] Output image filegif CompuServe GIF formatiris IRIS RGBps, epsf Encapsulated PostScriptmonops Monochrome PostScriptvectps 'Cartoon' PostScriptbmp Microsoft Bitmap formatpict Apple 'PICT' fileppm Portable Pixmap

sun, sunrle Sun Rasterfileset vectps Enable cartoon outlines

write script Generate RasMol scriptwrite povray Generate POVray datawrite vrml Generate VRMLdatawrite molscript

Output MolScript scriptwrite kinemage

Output Kinemage filesave Save selected atomsset kinemage Set Mage file detailset transparent Allow transparent GIFswrite phipsi Generate phi-psi datawrite RDF Ramachandran plot datawrite RPP Ramachandran printer

plot

Misc. Commands

structure DSSP secondry structureconnect [boolean] Recalculate connectivityrenumber Sequentially number chainsshow information Display molecule statisticsshow phipsi Display trosion anglesshow RPP Ramachandran printer plotshow sequence Display molecule sequenceshow symmetry Display crystal space groupset mouse rasmol Default mouse bindingsset mouse quanta Polygen's Quanta bindingsset mouse insight Biosym's Insight II bindingsset cisangle CIS angle cutoff

Command Line EditingIn addition to the cursor keys, the following 'emacs' control keys may be

used to edit the command line.

Ctrl-H / Ctrl-D Delete previous/next characterC t r l - B / C t r l - FMoveb a c k w a r d / f o r w ar d a characterCtrl-A / Ctrl-E Move to beginning/end of lineCtrl-P / Ctrl-N Display previous/next history

Colour Schemes

CPK Atom ColoursCarbon l ight grey [200,200,200]Oxygen red [240,0,0]Nitrogen sky b lue [143,143,255]Hydrogen white [255,255,255]Sulphur yellow [255,200,50]Phosphorous orange [255,165,0]Chlorine green [0,255,0]Bromine, Zinc brown [165,42,42]

Calcium dark grey [128,128,144]Unknown deep pink [255,20,147]

CPKnew Atom ColoursCarbon l ight grey [211,211,211]Oxygen red [255,0,0]Nitrogen sky b lue [135,206,235]Hydrogen white [255,255,255]Sulphur yellow [255,255,0]Phosphorous orange [255,170,0]Chlorine green [0,255,0]Bromine, Zinc brown [128,40,40]Calcium dark grey [105,105,105]Unknown deep pink [250,22,145]

Amino Acid ColoursASP, GLU bright red [230,10,10]CYS, MET yellow [230,230,0]LYS, ARG blue [20,90,255]SER, THR orange [250,150,0]PHE, TYR mid blue [50,50,170]ASN, GLN cyan [0,220,220]GLY light grey [235,235,235]LEU, VAL, ILE green [15,130,15]ALA dark grey [200,200,200]TRP pink [180,90,180]HIS p al e b lu e [1 30 ,1 30 ,2 10 ]PRO flesh [220,150,130]others tan [190,160,110]

Secondary Structure ColoursAlpha Helix magenta [240,0,128]Beta Sheet yellow [255,255,0]Turns p al e b lu e [9 6, 12 8, 25 5]Other white [255,255,255]

Hydrogen Bond Type ColoursOffset +2 white [255,255,255]Offset +3 magenta [255,0,255]Offset +4 red [255,0,0]Offset +5 orange [255,165,0]Offset -3 cyan [0,255,255]Offset -4 green [0,255,0]default yellow [255,255,0]