RasMol v2.7.2.1
Quick Reference Card	
©Copyright Roger Sayle 1992-1999
V2.6x1 Mods ©Copyright Arne Mueller1998; “ucb” Mods ©Copyright UC Regents/ModularCHEM 1995-1996; RasTop 1.3 ©Copyright  Philippe Valadon 2000; V2.7.2.1 ©Copyright Herbert J. Bernstein 1998-2001

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.

Mac	Windows	Action	
---	Left	Rotate X-Y	
Command	Right	Translate X-Y	
Shift	Shift Left	Zoom	
Shift-Cmnd	Shift Right	Rotate Z	
Control	Control Left	Z-Clipping (Slab)	

General Commands

load [format] <filename>	Load a molecule (up to 5)
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	
mopac	J.P. Stewart's MOPAC file format	
cif	IUCr CIF or mmCIF file format	

exit	Exit from RasMol Script
quit	Terminate pgm execution

help [topic [subtopic]]	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 <filename>	Execute file of commands

zap	Delete molecule

Bond Commands

bond <src> <dst> +	Add a bond
bond <src> <dst> pick
	Pick bond for rotation
unbond <src> <dst>	Remove a bond

Display Commands

wireframe [boolean]	Display wireframe 
wireframe <rad> [<rad>]	Display stick bonds
set bondmode all	Mark all atoms
set bondmode none	Mark no atoms
set bondmode not bonded	
	Mark non-bonded atoms

spacefill [boolean]	Display spacefill spheres
spacefill <value>	Specify atom sphere radius
spacefill temperature
spacefill user
star ...	Display stars for spheres

backbone [boolean]	Display alpha backbone
backbone <value>	Specify backbone radius

ribbons [boolean]	Display solid ribbons
ribbons <value>	Specify ribbon width

strands [boolean]	Draw ribbon as strands 
strands <value>	Specify ribbon width
set strands <value>	Number of ribbon strands

label [boolean]	Draw default atom labels 
label <string>	Label with arbitrary text
set fontsize <value> [FS|PS]
	Set label font height
set fontstroke<value>	Set label stroke width

ssbonds [boolean]	Display disulphide bonds
ssbonds <value>	Specify ssbond radius
set ssbonds backbone	SSBonds between alphas
set ssbonds sidechain	SSBonds between sulphurs

hbonds [boolean]	Display hydrogen bonds
hbonds <value>	Specify hbond radius
set hbonds backbone	HBonds between alphas
set hbonds sidechain	HBonds donor/acceptor

dots [boolean]	Display dot surface
dots <value>	Specify dot density

set solvent [boolean]	VDW or solvent surface
set radius <value>	Specify probe sphere rad.

set axes [boolean]	Display co-ordinate axes
set boundbox [boolean]
	Display bounding box
set unitcell [boolean]	Display crystal unit cell

set monitor [boolean]	Show distance monitor labels
set backfade [boolean]
	Shade to any background color
set display selected	Currently selected portion

set picking	Series of 13 commands:
	  off | ident | distance| angle
	  | torsion | label | monitor | center 
	  coord | bond | atom | group | chain

Colour Commands

colour [object] <colour>	Colour representation

Objects:
atoms	bonds	backbone	
ribbons	labels	hbonds	
ssbonds	dots	axes	
ribbons1	ribbons2		

Predefined Colours:
Black	Blue	BlueTint	Brown	
Cyan	Gold	Grey	Green	
GreenBlue	GreenTint	HotPink	Magenta	
Orange	Pink	PinkTint	Purple	
Red	RedOrange	SeaGreen	SkyBlue	
Violet	White	Yellow	YellowTont	

Atom Colour Schemes:
cpk	amino	shapely	
group	chain	structure	
temperature	charge	user	
alt	model		

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

Manipulation Commands

depth[boolean]	Enable/disable back-clipping
depth <value>	Move back-clipping plane

molecule <number>	Specify  molecule to manipulate

rotate <axis> [-] <value>	Rotate molecule
rotate bond		Rotate bond
rotate molecule		Rotate selected molecule
rotate all		Rotate all molecules

translate <axis> [-] <value>
		Translate molecule

zoom [boolean]	Scale molecule
zoom <value>		Specify  magnification

slab [boolean]	Enable/disable slabbing
slab <value>	Move Z-clipping plane

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

reset	Initial transformation

set stereo [boolean]	Control L&R images

Scripted Commands

load [format] inline	Load molecule 
	  from script
pause	Suspend script execution
echo	Display text on
	  command line
refresh	Redraw image
set write [boolean]	Save & write in scripts

Atom Expressions

Predefined Sets:	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	acidic	acyclic	aliphatic	
alpha	amino	aromatic	backbone	
basic	bonded	buried	cg	
charged	cyclic	cystine	helix	
hetero	hydrogen	hydrophobic	ions	
large	ligand	medium	neutral	
nucleic	polar	protein	purine	
pyrimidine	selected	sheet	sidechain	
small	solvent	surface	turn	
water				

define <identifier> <expression>	
			User-defined sets

Rendering Commands

background <colour>	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 shadepower [value]	Control atom 'contrast’

Language Commands

English	English menus and messages
French	French menus and messages
Italian	Italian menus and messages
Spanish	Spanish menus and messages

Export Commands

write [format] <filename>	Output image file
gif	CompuServe GIF format	
iris	IRIS RGB	
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 	

set vectps <boolean>	Enable cartoon outlines

write script <filename>	Generate RasMol script
write povray <filename>	Generate POVray data
write vrml<filename>	Generate VRMLdata
write molscript <filename>
	Output MolScript script
write kinemage <filename>
	Output Kinemage file
save <filename>	Save selected atoms
set kinemage <boolean>	Set Mage file detail
set transparent<boolean>	Allow transparent GIFs
write phipsi<filename>	Generate phi-psi data
write RDF<filename>	Ramachandran plot data
write RPP<filename>	Ramachandran printer 
	plot

Misc. Commands

structure	DSSP secondry structure
connect [boolean]	Recalculate connectivity
renumber	Sequentially number chains

show information	Display molecule statistics
show phipsi	Display trosion angles
show RPP	Ramachandran printer plot
show sequence	Display molecule sequence
show symmetry	Display crystal space group

set mouse rasmol	Default mouse bindings
set mouse quanta	Polygen's Quanta bindings
set mouse insight	Biosym's Insight II bindings

set cisangle	CIS angle cutoff

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	Delete previous/next character
Ctrl-B / Ctrl-F	Move backward/forward a character
Ctrl-A / Ctrl-E	Move to beginning/end of line
Ctrl-P / Ctrl-N	Display previous/next history

Colour Schemes

CPK Atom Colours
Carbon	light grey	[200,200,200]	
Oxygen	red	[240,0,0]	
Nitrogen	sky blue	[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]	

Amino Acid Colours
ASP, 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	pale blue	[130,130,210]	
PRO	flesh	[220,150,130]	
others	tan	[190,160,110]	

Secondary Structure Colours
Alpha Helix	magenta	[240,0,128]	
Beta Sheet	yellow	[255,255,0]	
Turns	pale blue	[96,128,255]	
Other	white	[255,255,255]	

Hydrogen Bond Type Colours
Offset +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]