Rasmol Reference Card

RasMol v2.5 Quick Reference Card (c) Copyright 1994 Roger Sayle

Mouse Buttons Clicking on an atom identifies that atom in the command window. Moving the mouse whilst holding mouse buttons and/or control keys manipulates the molecule. The default bindings are described below. RASWIN Left Button Right Button Shift Left Button Shift Right Button Control Left Button

RASMAC SINGLE BUTTON OPTION SHIFT SHIFT + OPTION CTRL

ACTION Rotate X-Y Translate X-Y Zoom Rotate Z Z-Clipping (Slab)

Display Commands

Colour Commands

wireframe [boolean] Display wireframe wireframe Display stick bonds

colour [object]

spacefill [boolean] Display spacefill spheres spacefill Specify atom sphere radius spacefill temperature spacefill user backbone [boolean] backbone

Display alpha backbone Specify backbone radius

ribbons [boolean] ribbons

Display solid ribbons Specify ribbon width

strands [boolean] strands set strands

Draw ribbon as strands Specify ribbon width Number of ribbon strands

label [boolean] Draw default atom labels label <string> Label with arbitrary text set fontsize Set label font height

General Commands

Objects: atoms ribbons ssbonds ribbons1

bonds labels dots ribbons2

Colour representation backbone hbonds axes

Predefined Colours: blue black cyan greenblue magenta orange red redorange v i o l e t yellow Atom Colour Schemes: cpk amino group chain temperature charge

shapely structure user

load [format] Load a molecule pdb Brookhaven Protein Databank mdl Molecular Design Limited's Mol file mol2 Tripos' Sybyl Mol2 file format alchemy Tripos' Alchemy file format charmm CHARMm format card file xyz MSC's XMOL XYZ file format

ssbonds [boolean] ssbonds

exit quit

set hbonds backbone HBonds between alphas set hbonds sidechain HBonds donor/acceptor

zoom [boolean] zoom

Scale molecule Specify magnification

dots [boolean] dots

slab [boolean] slab

Enable/disable slabbing Move Z-clipping plane

centre [expression]

Set centre of rotation

reset

Initial transformation

help [topic [subtopic]]

Exit from RasMol Display on-line help topic

select <expression> Update part of molecule restrict <expression> Display only part of mol. set bondmode [mode] Change bond selection script

Execute file of commands

zap

Delete molecule

set ssbonds backbone set ssbonds sidechain hbonds [boolean] hbonds

Display disulphide bonds Specify ssbond radius SSBonds between alphas SSBonds between sulphurs Display hydrogen bonds Specify hbond radius

Display dot surface Specify dot density

set solvent [boolean] VDW or solvent surface set radius Specify probe sphere rad. set axes [boolean] Display co-ordinate axes set boundbox [boolean] Display bounding box set unitcell [boolean] Display crystal unit cell

colour hbonds type colour dots potential

green purple white

Colour hbonds by offset Display potential surface

Manipulation Commands rotate [-] translate [-]

Rotate molecule

Translate molecul

Atom Expressions

Export Commands

Predefined Sets:

write [format] Output image file gif CompuServe GIF format ps, epsf Encapsulated PostScript monops Monochrome PostScript vectps 'Cartoon' PostScript bmp Microsoft Bitmap format pict Apple 'PICT' file ppm Portable Pixmap sun, sunrle Sun Rasterfile

alpha hydrophobic Residue Ranges: 3,16,12 9-20 Boolean Operators: backbone and not alpha ligand or 196-199 Primitive Expressions: cys, glu, arg, as? ser70a, **p, glu24:1 hem*p.fe, *.sg Comparison Operators: atomno=4,atomno=6 temperature>=900 Within Expressions: within(8.0,ligand)

Predefined Sets at alpha basic charged hetero large nucleic pyrimidine small water

acidic amino bonded cyclic hydrogen ligand polar selected solvent

acyclic aliphatic aromatic backbone buried cg cystine helix hydrophobici o n s medium neutral protein purine sheet sidechain surface turn

define <expression>

User-defined sets

Rendering Commands background

Set background colour

set ambient [value]

Depth-cueing/lighting

set shadows [boolean] Enable/disable shadows set specular [boolean] Enable atom highlights set specpower [value] Control atom 'shininess'

set vectps

Colour Schemes

Enable cartoon outlines

write script write molscript write kinemage set kinemage

Generate RasMol script Output MolScript script Output Kinemage file Set Mage file detail

Misc. Commands structure connect [boolean] renumber

DSSP secondry structure Recalculate connectivity Sequentially number chains

show information show sequence show symmetry

Display molecule statistics Display molecule sequence Display crystal space group

set mouse rasmol set mouse quanta set mouse insight

Default mouse bindings Polygen's Quanta bindings Biosym's Insight II bindings

Command Line Editing In addition to the cursor keys, the following 'emacs' control keys may be used to edit the command line. Ctrl-H / Ctrl-D Ctrl-B / Ctrl-F Ctrl-A / Ctrl-E Ctrl-P / Ctrl-N

Delete previous/next character Move backward/forward a character Move to beginning/end of line Display previous/next history

CPK Atom Colours Carbon Oxygen Nitrogen Hydrogen Sulphur Phosphorous Chlorine Calcium, Metals Unknown

light grey red light blue white yellow orange green dark grey deep pink

[200,200,200] [240,0,0] [143,143,255] [255,255,255] [255,200,50] [255,165,0] [0,255,0] [128,128,144] [255,20,147]

Amino Acid Colours ASP, GLU CYS, MET LYS, ARG SER, THR PHE, TYR ASN, GLN GLY LEU, VAL, ILE ALA TRP HIS PRO

bright red yellow blue orange mid blue cyan light grey green dark grey pink pale blue flesh

[230,10,10] [230,230,0] [20,90,255] [250,150,0] [50,50,170] [0,220,220] [235,235,235] [15,130,15] [200,200,200] [180,90,180] [130,130,210] [220,150,130]

Secondary Structure Colours Alpha Helix Beta Sheet Turns Other

magenta yellow pale blue white

[240,0,128] [255,255,0] [96,128,255] [255,255,255]

Hydrogen Bond Type Colours Offset +2 Offset +3 Offset +4 Offset +5 Offset -3 Offset -4 default

white magenta red orange cyan green yellow

[255,255,255] [255,0,255] [255,0,0] [255,165,0] [0,255,255] [0,255,0] [255,255,0]