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#{\footnote rasmol}
${\footnote RasMol V2.6}
+{\footnote doc}
\par{\fs28\b RasMol V2.6}\par\par
{\fs24\b Molecular Visualisation Program}\par\par
{\b Roger Sayle}\par
{\b Glaxo Wellcome Research and Development}\line
{\b Stevenage, Hertfordshire, U.K.}\par\par
\par{\fs24\b Table of Contents}\par\par
\tx250\li250\fi-250
{\f1\'b7}\tab
{\uldb Introduction}{\v chintro}\par
{\f1\'b7}\tab
{\uldb Command Reference}{\v chcomref}\par
{\f1\'b7}\tab
{\uldb Internal Parameters}{\v chsetopt}\par
{\f1\'b7}\tab
{\uldb Atom Expressions}{\v chexprs}\par
{\f1\'b7}\tab
{\uldb Predefined Sets}{\v predefinedsets}\par
{\f1\'b7}\tab
{\uldb Colour Schemes}{\v chcolours}\par
\pard
\par\page\par
+{\footnote doc}
Copyright \'a9 1992-1995 by Roger Sayle (rasmol@ggr.co.uk) {}
\par\par
{\fs16
The information supplied in this document is believed to be true but {}
no liability is assumed for its use or for the infringements of the {}
rights of the others resulting from its use. {}
\par\par
Information in this document is subject to change without notice and does {}
not represent a commitment on the part of the supplier. This package is {}
sold/distributed subject to the condition that it shall not, by way of {}
trade or otherwise, be lent, re-sold, hired out or otherwise circulated {}
without the supplier's prior consent, in any form of packaging or cover {}
other than that in which it was produced. No part of this manual or {}
accompanying software may be reproduced, stored in a retrieval system on {}
optical or magnetic disk, tape or any other medium, or transmitted in any {}
form or by any means, electronic, mechanical, photocopying, recording or {}
otherwise for any purpose other than the purchaser's personal use. {}
\par\par
This product is not to be used in the planning, construction, maintenance, {}
operation or use of any nuclear facility nor the flight, navigation or {}
communication of aircraft or ground support equipment. The author shall {}
not be liable, in whole or in part, for any claims or damages arising {}
from such use, including death, bancruptcy or outbreak of war. {}
}
\par\page\par
+{\footnote doc}
#{\footnote chintro}
${\footnote Introduction}
{\fs24\b Introduction}\par\par
RasMol2 is a molecular graphics program intended for the visualisation of {}
proteins, nucleic acids and small molecules. The program is aimed at {}
display, teaching and generation of publication quality images. RasMol {}
runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The {}
UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display {}
(X11R4 or later). The program reads in a molecule co-ordinate file and {}
interactively displays the molecule on the screen in a variety of colour {}
schemes and molecule representations. Currently available representations {}
include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, {}
ball and stick, solid and strand biomolecular ribbons, atom labels and dot {}
surfaces. {}
\par\page\par
+{\footnote doc}
#{\footnote chcomref}
${\footnote Command Reference}
{\fs24\b Command Reference}\par\par
RasMol allows the execution of interactive commands typed at the {}
"{\f2\b RasMol>}" {}
prompt in the terminal window. Each command must be given on {}
a separate line. Keywords are case insensitive and may be entered in {}
either upper or lower case letters. All whitespace characters are {}
ignored except to separate keywords and their arguments. {}
\par\par
The commands/keywords currently recognised by RasMol are given below. {}
\par\par
\cellx1200\cellx2400\cellx3600\cellx4800
\intbl
{\uldb backbone}{\v backbone}\cell
{\uldb background}{\v background}\cell
{\uldb centre}{\v centre}\cell
{\uldb clipboard}{\v clipboard}\cell
\row\intbl
{\uldb colour}{\v colour}\cell
{\uldb connect}{\v connect}\cell
{\uldb cpk}{\v cpk}\cell
{\uldb dots}{\v dots}\cell
\row\intbl
{\uldb define}{\v define}\cell
{\uldb echo}{\v echo}\cell
{\uldb exit}{\v exit}\cell
{\uldb hbonds}{\v hbonds}\cell
\row\intbl
{\uldb help}{\v help}\cell
{\uldb label}{\v label}\cell
{\uldb load}{\v load}\cell
{\uldb print}{\v print}\cell
\row\intbl
{\uldb quit}{\v quit}\cell
{\uldb renumber}{\v renumber}\cell
{\uldb reset}{\v reset}\cell
{\uldb restrict}{\v restrict}\cell
\row\intbl
{\uldb ribbon}{\v ribbon}\cell
{\uldb rotate}{\v rotate}\cell
{\uldb save}{\v save}\cell
{\uldb script}{\v script}\cell
\row\intbl
{\uldb select}{\v select}\cell
{\uldb set}{\v set}\cell
{\uldb show}{\v show}\cell
{\uldb slab}{\v slab}\cell
\row\intbl
{\uldb source}{\v source}\cell
{\uldb spacefill}{\v spacefill}\cell
{\uldb ssbonds}{\v ssbonds}\cell
{\uldb strands}{\v strands}\cell
\row\intbl
{\uldb structure}{\v structure}\cell
{\uldb trace}{\v trace}\cell
{\uldb translate}{\v translate}\cell
{\uldb wireframe}{\v wireframe}\cell
\row\intbl
{\uldb write}{\v write}\cell
{\uldb zap}{\v zap}\cell
{\uldb zoom}{\v zoom}\cell
\row\pard\par\trowd
\par\page\par
+{\footnote doc}
#{\footnote trace}
#{\footnote backbone}
${\footnote Backbone}
K{\footnote backbone}
{\b Backbone}\par\par
\tx1200
{\f2\b Syntax:\tab
backbone \{\}\line\tab
backbone \par
}\pard\par
The RasMol {}
{\f2\b backbone} {}
command permits the representation of a polypeptide {}
backbone as a series of bonds connecting the adjacent alpha carbons of {}
each amino acid in a chain. The display of these backbone `bonds' is {}
turned on and off by the command paramater the same as the {}
{\uldb wireframe}{\v wireframe} {}
command. The command {}
{\f2\b backbone off} {}
turns off the selected `bonds', and {}
{\f2\b backbone on} {}
or with a number turns them on. The number can be used {}
to specify the cylinder radius of the representation in either angstrom {}
or rasmol units. A parameter value of 500 (2.0 angstroms) or above {}
results in a "Parameter value too large" error. Backbone objects may be {}
coloured using the RasMol {}
{\uldb colour backbone}{\v colour} {}
command. {}
\par\par
The reserved work {}
{\f2\b backbone} {}
is also used as a predefined set and as a parameter to the {}
{\f2\b set hbond} {}
and {}
{\f2\b set ssbond} {}
commands. The RasMol command {}
{\f2\b trace} {}
is synonymous with the command {}
{\f2\b backbone.} {}
\par\page\par
+{\footnote doc}
#{\footnote background}
${\footnote Background}
K{\footnote background}
{\b Background}\par\par
\tx1200
{\f2\b Syntax:\tab
background \par
}\pard\par
The RasMol {}
{\f2\b background} {}
command is used to set the colour of the "canvas" background. The {}
colour may be given as either a colour name or a comma separated {}
triple of Red, Green and Blue (RGB) components enclosed in square {}
brackets. Typing the command {}
{\uldb help colours}{\v help} {}
will give a list of the predefined colour names recognised by RasMol. {}
When running under X Windows, RasMol also recognises colours in the {}
X server's colour name database. {}
\par\par
The {}
{\f2\b background} {}
command is synonymous with the RasMol {}
{\uldb set background}{\v setbackground} {}
command. {}
\par\page\par
+{\footnote doc}
#{\footnote center}
#{\footnote centre}
${\footnote Centre}
K{\footnote centre}
{\b Centre}\par\par
\tx1200
{\f2\b Syntax:\tab
center \{\}\line\tab
centre \{\}\par
}\pard\par
The RasMol {}
{\f2\b centre} {}
command defines the point about which the {}
{\uldb rotate}{\v rotate} {}
command and the scroll bars rotate the current molecule. Without a {}
parameter the centre command resets the centre of rotation to be the {}
centre of gravity of the molecule. If an atom expression is specified, {}
RasMol rotates the molecule about the centre of gravity of the set of {}
atoms specified by the expression. Hence, if a single atom is specified {}
by the expression, that atom will remain `stationary' during rotations. {}
\par\par
Type {}
{\uldb help expression}{\v help} {}
for more information on RasMol atom expressions. {}
\par\page\par
+{\footnote doc}
#{\footnote clipboard}
${\footnote Clipboard}
K{\footnote clipboard}
{\b Clipboard}\par\par
\tx1200
{\f2\b Syntax:\tab
clipboard\par
}\pard\par
The RasMol {}
{\f2\b clipboard} {}
command places a copy of the currently displayed image on the local {}
graphics `clipboard'. Note: this command is not yet supported on {}
UNIX or VMS machines. It is intended to make transfering images {}
between applications easier under Microsoft Windows or on an Apple {}
Macintosh. {}
\par\par
When using RasMol on a UNIX or VMS system this functionality may be {}
achieved by generating a raster image in a format that can be read {}
by the receiving program using the RasMol {}
{\uldb write}{\v write} {}
command. {}
\par\page\par
+{\footnote doc}
#{\footnote color}
#{\footnote colour}
${\footnote Colour}
K{\footnote colour}
{\b Colour}\par\par
\tx1200
{\f2\b Syntax:\tab
colour \{