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%% RasMol V2.30 Manual %% (c) Roger Sayle, January 1994 %% Glaxo Research and Development %% Greenford, Middlesex %% %% %% UNIX man(1) Headers %% MR.PU MR.TH RASMOL 1 "January 1994" MR.SH NAME MRRasMol 2.3 \- Molecular Graphics Visualisation Tool %% %% RTF Headers %% RR{\rtf1\ansi RR{\fonttbl RR\f0\fswiss Arial; RR\f1\fdecor Symbol; RR\f2\fmodern Courier New; RR}\deff0\fs20 RR#{\footnote rasmol} RR${\footnote RasMol V2.3} RR+{\footnote doc} RR\par{\fs28\b RasMol V2.3}\par\par RR{\fs24\b Molecular Visualisation Program}\par\par RR{\b Roger Sayle}\par RR{\b Glaxo Research and Development}\line RR{\b Greenford, Middlesex, U.K.}\par\par %% %% HTML Headers %% HR<title>RasMol V2.3 Molecular Visualisation Program</title> HR<h1>RasMol V2.3</h1><p> HR<h2>Molecular Visualisation Program</h2><p> HR<h3>Roger Sayle</h3> HR<h3>Glaxo Research and Development</h3> HR<h3>Greenford, Middlesex, U.K.</h3><p><p> %% %% HTML Table of Contents %% HR<h2>Table of Contents</h2> HR<ol> HR<li><a href="#chintro">Introduction</a> HR<li><a href="#chcomref">Command Reference</a> HR<li><a href="#chsetopt">Internal Parameters</a> HR<li><a href="#chexprs">Atom Expressions</a> HR<li><a href="#predefinedsets">Predefined Sets</a> HR<li><a href="#chcolours">Colour Schemes</a> HR</ol> RR\par{\fs24\b Table of Contents}\par\par RR\tx250\li250\fi-250 RR{\f1\'b7}\tab RR{\uldb Introduction}{\v chintro}\par RR{\f1\'b7}\tab RR{\uldb Command Reference}{\v chcomref}\par RR{\f1\'b7}\tab RR{\uldb Internal Parameters}{\v chsetopt}\par RR{\f1\'b7}\tab RR{\uldb Atom Expressions}{\v chexprs}\par RR{\f1\'b7}\tab RR{\uldb Predefined Sets}{\v predefinedsets}\par RR{\f1\'b7}\tab RR{\uldb Colour Schemes}{\v chcolours}\par RR\pard AB %% %% Copyright Notices %% TTCopyright (C) 1992,1993,1994 by Roger Sayle (rasmol@ggr.co.uk) RTCopyright \'a9 1992,1993,1994 by Roger Sayle (rasmol@ggr.co.uk) HT<p><p>Copyright (c) 1992,1993,1994 by Roger Sayle HT<address>rasmol@ggr.co.uk</address> AP RR{\fs16 VTThe information supplied in this document is believed to be true but VTno liability is assumed for its use or for the infringements of the VTrights of the others resulting from its use. VP VTInformation in this document is subject to change without notice and does VTnot represent a commitment on the part of the supplier. This package is VTsold/distributed subject to the condition that it shall not, by way of VTtrade or otherwise, be lent, re-sold, hired out or otherwise circulated VTwithout the supplier's prior consent, in any form of packaging or cover VTother than that in which it was produced. No part of this manual or VTaccompanying software may be reproduced, stored in a retrieval system on VToptical or magnetic disk, tape or any other medium, or transmitted in any VTform or by any means, electronic, mechanical, photocopying, recording or VTotherwise for any purpose other than the purchaser's personal use. VP VTThis product is not to be used in the planning, construction, maintenance, VToperation or use of any nuclear facility nor the flight, navigation or VTcommunication of aircraft or ground support equipment. The author shall VTnot be liable, in whole or in part, for any claims or damages arising VTfrom such use, including death, bancruptcy or outbreak of war. RR} AB %% %% Man Page Synopsis %% MR.SH SYNOPSIS MR.B rasmol MR.RB [ options ] MR[ MR.I pdbfile MR] %% %% Simple Description %% TR INTRODUCTION TR ============ TR RR#{\footnote chintro} RR${\footnote Introduction} RR{\fs24\b Introduction}\par\par MR.SH DESCRIPTION HR<a name="chintro"><h2>Introduction</h2></a> ATRasMol2 is an X11 windows system tool intended for the visualisation of ATproteins and nucleic acids. RasMol requires either an 8bit pseudo colour ATor a 24bit (32bit) true colour display. The program reads in a specified ATBrookhaven protein databank (PDB) file and determines the connectivity from ATthe residue information provided. This may then rendered on the screen ATin a variety of formats and colour schemes. Currently available molecule ATrepresentations include depth-cued wireframes, sticks, space filling `union ATof spheres', ball and stick models and protein ribbon diagrams. PP PRThe RasMol help facility can be accessed by typing "help <topic>" or PR"help <topic> <subtopic>" from the command line. A complete list of RasMol PRcommands may be displayed by typing "help commands". A single question PRmark may also be used to abbreviate the keyword "help". PR PRCopyright (c) 1992-1994 by Roger Sayle (ras32425@ggr.co.uk) AB %% %% Commands Introduction %% RR#{\footnote chcomref} RR${\footnote Command Reference} RR{\fs24\b Command Reference}\par\par MR.SH COMMANDS PR?commands PR?keywords HR<a name="chcomref"><h2>Command Reference</h2></a> TR COMMANDS TR ======== TR ATRasMol allows the execution of interactive commands typed at the AC"RasMol> ATprompt in the terminal window. Each command must be given on ATa separate line. Keywords are case insensitive and may be entered in ATeither upper or lower case letters. All whitespace characters are ATignored except to separate keywords and their arguments. AP ATThe commands/keywords currently recognised by RasMol are given below. PRType "help <command>" for more information on each RasMol function. AP PR backbone colour exit hbond PR help load quit reset PR restrict ribbon rotate save PR script select set show PR slab spacefill structure ssbond PR translate wireframe write zap PR zoom PP HR<pre> HR <a href="#backbone">Backbone</a HR> <a href="#background">Background</a HR> <a href="#centre">Centre</a> HR <a href="#colour">Colour</a HR> <a href="#hbonds">HBonds</a HR> <a href="#help">Help</a> HR <a href="#load">Load</a HR> <a href="#quit">Quit</a HR> <a href="#renumber">Renumber</a> HR <a href="#reset">Reset</a HR> <a href="#restrict">Restrict</a HR> <a href="#ribbons">Ribbons</a> HR <a href="#rotate">Rotate</a HR> <a href="#save">Save</a HR> <a href="#script">Script</a> HR <a href="#select">Select</a HR> <a href="#set">Set</a HR> <a href="#show">Show</a> HR <a href="#slab">Slab</a HR> <a href="#spacefill">Spacefill</a HR> <a href="#structure">Structure</a> HR <a href="#ssbonds">SSBonds</a HR> <a href="#translate">Translate</a HR> <a href="#wireframe">Wireframe</a> HR <a href="#write">Write</a HR> <a href="#zap">Zap</a HR> <a href="#zoom">Zoom</a> HR</pre><hr> RR\cellx1200\cellx2400\cellx3600\cellx4800 RR\intbl RR{\uldb backbone}{\v backbone}\cell RR{\uldb colour}{\v colour}\cell RR{\uldb exit}{\v exit}\cell RR{\uldb hbond}{\v hbond}\cell RR\row\intbl RR{\uldb help}{\v help}\cell RR{\uldb load}{\v load}\cell RR{\uldb quit}{\v quit}\cell RR{\uldb reset}{\v reset}\cell RR\row\intbl RR{\uldb restrict}{\v restrict}\cell RR{\uldb ribbon}{\v ribbon}\cell RR{\uldb rotate}{\v rotate}\cell RR{\uldb save}{\v save}\cell RR\row\intbl RR{\uldb script}{\v script}\cell RR{\uldb select}{\v select}\cell RR{\uldb set}{\v set}\cell RR{\uldb show}{\v show}\cell RR\row\intbl RR{\uldb slab}{\v slab}\cell RR{\uldb spacefill}{\v spacefill}\cell RR{\uldb structure}{\v structure}\cell RR{\uldb ssbond}{\v ssbond}\cell RR\row\intbl RR{\uldb translate}{\v translate}\cell RR{\uldb wireframe}{\v wireframe}\cell RR{\uldb write}{\v write}\cell RR{\uldb zap}{\v zap}\cell RR{\uldb zoom}{\v zoom}\cell RR\row\pard\par RB %% %% Commands Reference %% ASBackbone NRSyntax: backbone {<boolean>} NR backbone <value> NR HR<pre> HRSyntax: backbone {<boolean>} HR backbone <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRbackbone \{<boolean>\}\line\tab RRbackbone <value>\par RR}\pard\par ATThe RasMol ACbackbone ATcommand permits the representation of a polypeptide ATbackbone as a series of bonds connecting the adjacent alpha carbons of ATeach amino acid in a chain. The display of these backbone `bonds' is ATturned on and off by the command paramater the same as the AXwireframe wireframe ATcommand. The command ACbackbone off ATturns off the selected `bonds', and ACbackbone on ATor with a number turns them on. The number can be used ATto determine the cylinder radius of the representation in 0.004 angstrom ATunits. Backbone objects may be coloured using the RasMol AXcolour colour backbone ATcommand. A parameter value of 500 (2 angstroms) or above results in an AT"Integer argument too large" error. PP PTThe reserved work backbone is also used as a predefined set ("help sets") PTand as a parameter to the `set hbond' and `set ssbond' commands. AB ASBackground NRSyntax: background <colour> NR HR<pre> HRSyntax: background <colour> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRbackground <colour>\par RR}\pard\par ATThe RasMol ACbackground ATcommand is used to set the colour of the "canvas" background. The ATcolour may be given as either a colour name or a comma separated ATtriple of Red, Green and Blue (RGB) components enclosed in square ATbrackets. Typing the command AXhelp help colours ATwill give a list of the predefined colour names recognised by RasMol. ATWhen running under X Windows, RasMol also recognises colours in the ATX server's colour name database. AB PR?center RR#{\footnote center} ASCentre NRSyntax: center {<expression>} NR centre {<expression>} NR HR<pre> HRSyntax: center {<expression>} HR centre {<expression>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRcenter \{<expression>\}\line\tab RRcentre \{<expression>\}\par RR}\pard\par ATThe RasMol ACcentre ATcommand defines the point about which the AXrotate rotate ATcommand and the scroll bars rotate the current molecule. Without a ATparameter the centre command resets the centre of rotation to be the ATcentre of gravity of the molecule. If an atom expression is specified, ATRasMol rotates the molecule about the centre of gravity of the set of ATatoms specified by the expression. Hence, if a single atom is specified ATby the expression, that atom will remain `stationary' during rotations. AP ATType AXhelp help expression ATfor more information on RasMol atom expressions. AB PR?color RR#{\footnote color} ASColour NRSyntax: colour {<object>} <colour> NR color {<object>} <colour> NR HR<pre> HRSyntax: colour {<object>} <colour> HR color {<object>} <colour> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRcolour \{<object>\} <colour>\line\tab RRcolor \{<object>\} <colour>\par RR}\pard\par ATColour the atoms (or other objects) of the selected zone. The colour may ATbe given as either a colour name or a comma separated triple of Red, Green ATand Blue (RGB) components enclosed in square brackets. Typing the command AXhelp help colours ATwill give a list of all the predefined colour names recognised ATby RasMol. AP ATAllowed objects are ACatoms, ACbonds, AXbackbone backbone, AXhbonds hbonds, AXribbons ribbons ATand AXssbonds ssbonds. ATIf no object is specified, the default keyword ACatom ATis assumed. ATSome colour schemes are defined for certain object types. The colour scheme ACnone ATcan be applied all objects accept atoms, stating that the selected ATobjects have no colour of their own, but use the colour of their associated ATatoms (i.e. the atoms they connect). ACAtom ATobjects can also be coloured by AXaminocolours amino, AXcpkcolours cpk, AXchaincolours chain, AXgroupcolours group, AXshapelycolours shapely, AXstructurecolours structure, AXtemperaturecolours temperature ATand AXusercolours user ATand hydrogen bond objects can also be coloured by AXhbondtypecolours type. ATFor more information type AXchcolours help colour <colour>. AB PR?hbond RR#{\footnote hbond} ASHBonds NRSyntax: hbonds {<boolean>} NR hbonds <value> NR HR<pre> HRSyntax: hbonds {<boolean>} HR hbonds <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRhbonds \{<boolean>\}\line\tab RRhbonds <value>\par RR}\pard\par ATThe RasMol AChbond ATcommand is used to represent the hydrogen bonding of the protein ATmolecule's backbone. This information is useful in assessing the ATprotein's secondary structure. Hydrogen bonds are represented as ATeither dotted lines or cylinders between the donor and acceptor ATresidues. The first time the AChbond ATcommand is used, the program searches the structure of the ATmolecule to find hydrogen bonded residues and reports the number of bonds ATto the user. The command AChbonds on ATdisplays the selected `bonds' as dotted lines, and the AChbonds off ATturns off their display. The colour of hbond objects may be changed ATby the AXcolour colour hbond ATcommand. Initially, each hydrogen bond has the colours of its connected ATatoms. AP ATBy default the dotted lines are drawn between the accepting oxygen and ATthe donating nitrogen. By using the AXsethbonds set hbonds ATcommand the alpha carbon positions of the appropriate residues may be ATused instead. This is especially useful when examining proteins in ATbackbone representation. AB ASHelp NRSyntax: help {<topic> {<subtopic>}} NR ? {<topic> {<subtopic>} NR HR<pre> HRSyntax: help {<topic> {<subtopic>}} HR ? {<topic> {<subtopic>}} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRhelp \{<topic> \{<subtopic>\}\}\line\tab RR? \{<topic> \{<subtopic>\}\}\par RR}\pard\par ATThe RasMol AChelp ATcommand provides on-line help on the given topic. AB ASLoad NRSyntax: load {pdb} <filename> NR load alchemy <filename> NR HR<pre> HRSyntax: load {pdb} <filename> HR load alchemy <filename> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRload \{pdb\} <filename>\line\tab RRload alchemy <filename>\par RR}\pard\par ATLoad either a Brookhaven Protein Databank (PDB) file or Alchemy(tm) format ATfile into RasMol2. Only a single PDB file may be loaded at a time. This ATcommand selects all the atoms in the molecule, and sets the default ATrepresentation to be a cpk coloured wireframe model. AB PR?exit RR#{\footnote exit} ASQuit NRSyntax: quit NR exit NR HR<pre> HRSyntax: quit HR exit HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRquit\line\tab RRexit\par RR}\pard\par ATExit from the RasMol program. AB PR?renum RR#{\footnote renum} ASRenumber NRSyntax: renumber {{-} <value>} NR HR<pre> HRSyntax: renumber {{-} <value>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRrenumber \{\{-\} <value>\}\par RR}\pard\par ATThe RasMol ACrenumber ATcommand sequentially numbers the residues in a macromolecular chain. ATThe optional parameter specifies the value of the first residue in the ATsequence. By default, this value is one. For proteins, ATeach amino acid is numbered consecutively from the N terminus to the C ATterminus. For nucleic acids, each base is numbered from the 5' terminus ATto 3' terminus. All chains in the current database are renumbered and gaps ATin the original sequence are ignored. The starting value for numbering may ATbe negative. AB ASReset NRSyntax: reset NR HR<pre> HRSyntax: reset HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRreset\par RR}\pard\par ATThe RasMol ACreset ATcommand restores the original viewing transformation ATand centre of rotation. The scale is set to it default value, AXzoom zoom 100, ATthe centre of rotation is set to the geometric centre of the currently ATloaded molecule, AXcentre centre all, ATthis centre is translated to the middle of the screen and ATthe viewpoint set to the default orientation. AP ATThis command should not be mistaken for the RasMol AXzap zap ATcommand which deletes the currently stored molecule, returning the ATprogram to its initial state. AB ASRestrict NRSyntax: restrict {<expression>} NR HR<pre> HRSyntax: restrict {<expression>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRrestrict \{<expression>\}\par RR}\pard\par ATThe RasMol ACrestrict ATcommand both defines the currently active zone of the ATmolecule and disables the representation of (most of) those parts of the ATmolecule no longer selected. All subsequent RasMol commands that modify ATa molecule's colour or representation effect only the currently selected ATzone. The parameter of a ACrestrict ATcommand is a RasMol atom expression that is evaluated for every atom ATof the current molecule. This command is very similar to the RasMol AXselect select ATcommand, except restrict disables the AXwireframe wireframe, AXspacefill spacefill ATand AXbackbone backbone ATrepresentations in the non-active zone. AP ATType "help expression" for more information on RasMol atom expressions. AB PR?ribbon RR#{\footnote ribbon} ASRibbons NRSyntax: ribbons {<boolean>} NR ribbons <value> NR HR<pre> HRSyntax: ribbons {<boolean>} HR ribbons <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRribbons \{<boolean>\}\line\tab RRribbons <value>\par RR}\pard\par ATThe RasMol ACribbons ATcommand displays the currently loaded protein as a smooth "ribbon" ATof depth-cued curves passing along the backbone of the protein. The ATribbon is composed of a number of strands that run parallel to one ATanother along the peptide plane of each residue. The ribbon is drawn ATbetween each amino acid whose alpha carbon is currently selected. ATThe colour of the ribbon is changed by the RasMol AXcolour colour ribbon ATcommand. If the current ribbon colour is ACnone AT(the default), the colour is taken from the alpha carbon at each ATposition along its length. AP ATThe width of the ribbon at each position is determined by the optional ATparameter in the usual RasMol units. By default this value is 380, which ATproduces a ribbon 1.52 Angstroms wide. The number of strands in the ATribbon may be altered using the RasMol AXsetstrands set strands ATcommand. The rendering of the ribbon may also be changed using the AXsetribbons set ribbons ATcommand. AB ASRotate NRSyntax: rotate <axis> {-} <value> NR HR<pre> HRSyntax: rotate <axis> {-} <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRrotate <axis> \{-\} <value>\par RR}\pard\par ATRotate the molecule about the specified axis. ATPermited values for the axis parameter are HT"<tt><b>x</b></tt>", "<tt><b>y</b></tt>" and "<tt><b>z</b></tt>". RT"{\f2\b x}", "{\f2\b y}" and "{\f2\b z}". MT"x", "y" and "z". NT"x", "y" and "z". ATThe integer parameter states the angle in degrees for the structure to ATbe rotated. For the X and Y axes, positive values move the closest point ATup and right, and negative values move it down and left respectively. For ATthe Z axis, a positive rotation acts clockwise and a negative angle ATanti-clockwise. AB ASSave NRSyntax: save {pdb} <filename> NR save alchemy <filename> NR HR<pre> HRSyntax: save {pdb} <filename> HR save alchemy <filename> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRsave \{pdb\} <filename>\line\tab RRsave alchemy <filename>\par RR}\pard\par ATSave the currently selected set of atoms in either a Brookhaven Protein ATDatabase (PDB) or Alchemy(tm) format file. This command should not be ATconfused with the RasMol AXwrite write ATcommand which generates either image or script files. AB ASScript NRSyntax: script <filename> NR HR<pre> HRSyntax: script <filename> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRscript <filename>\par RR}\pard\par ATThe RasMol ACscript ATcommand reads a set of commands sequentially from a ATtext file and executes them. This allows sequences of commonly used ATcommands to be stored and performed by a single command. A RasMol script ATfile may contain a further script command up to a maximum "depth" of 10, ATallowing compilicated sequences of actions to be executed. AB ASSelect NRSyntax: select {<expression>} NR HR<pre> HRSyntax: select {<expression>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRselect \{<expression>\}\par RR}\pard\par ATDefine the currently active zone of the molecule. All subsequent RasMol ATcommands that manipulate a molecule or modify its colour or representation, ATonly effects the currently selected zone. The parameter of a ACselect ATcommand is a RasMol expression that is evaluated for every atom of the ATcurrent molecule. The currently selected (active) zone of the molecule ATare those atoms that cause the expression to evaluate true. To select ATthe whole molecule use the RasMol command ACselect all. AP ATType "help expression" for more information on RasMol atom expressions. AB ASSet NRSyntax: set <parameter> {<option>} NR HR<pre> HRSyntax: set <parameter> {<option>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset <parameter> \{<option>\}\par RR}\pard\par ATThe RasMol ACset ATcommand allows the user to alter various internal program parameters ATsuch as those controlling rendering options. Each parameter has its ATown set or permissible parameter options. Typically, ommiting the ATparamter option resets that parameter to its default value. A list of ATvalid parameter names is given below. For more information on each ATinternal parameter type AXhelp help set <parameter>. AP PR ambient background bondmode display PR hbond hetero hourglass hydrogen PR mouse ribbons shadow slabmode PR specular specpower ssbonds strands HR<pre> HR <a href="#setambient">Ambient</a HR> <a href="#setbackground">Background</a HR> <a href="#setbondmode">BondMode</a> HR <a href="#sethbonds">HBonds</a HR> <a href="#sethetero">Hetero</a HR> <a href="#sethourglass">HourGlass</a> HR <a href="#sethydrogen">Hydrogen</a HR> <a href="#setmouse">Mouse</a HR> <a href="#setshadow">Shadow</a> HR <a href="#setslabmode">SlabMode</a HR> <a href="#setspecular">Specular</a HR> <a href="#setspecpower">SpecPower</a> HR <a href="#setssbonds">SSBonds</a HR> <a href="#setstrands">Strands</a> HR</pre> RR\cellx1200\cellx2400\cellx3600\cellx4800 RR\intbl RR{\uldb ambient}{\v setambient}\cell RR{\uldb background}{\v setbackground}\cell RR{\uldb bondmode}{\v setbondmode}\cell RR{\uldb hbonds}{\v sethbonds}\cell RR\row\intbl RR{\uldb hetero}{\v sethetero}\cell RR{\uldb hourglass}{\v sethourglass}\cell RR{\uldb hydrogen}{\v sethydrogen}\cell RR{\uldb mouse}{\v setmouse}\cell RR\row\intbl RR{\uldb shadow}{\v setshadow}\cell RR{\uldb slabmode}{\v setslabmode}\cell RR{\uldb specular}{\v setspecular}\cell RR{\uldb specpower}{\v setspecpower}\cell RR\row\intbl RR{\uldb ssbonds}{\v setssbonds}\cell RR{\uldb strands}{\v setstrands}\cell RR\row\pard\par AB ASShow NRSyntax: show information NR show sequence NR HR<pre> HRSyntax: show information HR show sequence HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRshow information\line\tab RRshow sequence\par RR}\pard\par ATThe RasMol ACshow ATcommand display details of the status of the currently ATloaded molecule. The command ACshow information ATlists the molecule's name, ATclassification, PDB code and the number of atoms, chains, groups it contains. ATIf hydrogen bonding, disulphide bridges or secondary structure have been ATdetermined, the number of hbonds, ssbonds, helices, ladders and turns ATare also displayed respectively. The command ACshow sequence ATlists the residues that compose each chain of the molecule. AB ASSlab NRSyntax: slab {<boolean>} NR slab <value> NR HR<pre> HRSyntax: slab {<boolean>} HR slab <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRslab \{<boolean>\}\line\tab RRslab <value>\par RR}\pard\par ATThe RasMol ACslab ATcommand enables, disables or positions the z-clipping plane of the ATmolecule. The program only draws those portions of the ATmolecule that are further from the viewer than the slabbing plane. ATInteger values range from zero at the very back of the molecule to AT100 which is completely in front of the molecule. Intermediate values ATdetermine the percentage of the molecule to be drawn. AB ASSpacefill NRSyntax: spacefill {<boolean>} NR spacefill temperature NR spacefill user NR spacefill <value> NR HR<pre> HRSyntax: spacefill {<boolean>} HR spacefill temperature HR spacefill user HR spacefill <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRspacefill \{<boolean>\}\line\tab RRspacefill temperature\line\tab RRspacefill user\line\tab RRspacefill <value>\par RR}\pard\par ATRepresent the currently selected zone as a spacefilling union of spheres ATmodel. An integer parameter may be used to specify the radius of each ATatom given in 4nm units. If no parameter is given, each atom is drawn as ATa sphere of its Van der Waals radius. AP ATThe ACtemperature AToption is used to set the radius of each selected sphere ATto the value in the temperature field of the molecule file. A zero or ATnegative value causes no change in the selected atom. Temperature values ATgreater than 2.00 are truncated to 2.00 Angstrom radius. AP ATThe ACuser AToption allows the radius of the selected spheres to be determined ATby matching each atom against optional lines in the input data file. Details ATof the wildcard pattern matching used by Raster3D's COLOR records is given ATin the manual. AB PR?ssbond RR#{\footnote ssbond} ASSSBonds NRSyntax: ssbonds {<boolean>} NR ssbonds <value> NR HR<pre> HRSyntax: ssbonds {<boolean>} HR ssbonds <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRssbonds \{<boolean>\}\line\tab RRssbonds <value>\par RR}\pard\par ATThe RasMol ACssbonds ATcommand is used to represent the disulphide bridges of the protein ATmolecule as either dotted lines or cylinders between the connected ATcysteines. The first time that the ACssbonds ATcommand is used, the program searches the structure of the protein to ATfind half-cysteine pairs (cysteines whose sulphurs are within 3 angstroms ATof each other) and reports the number of bridges to the user. The command ACssbonds on ATdisplays the selected `bonds' as dotted lines, and the command ACssbonds off ATdisables the display of ssbonds in the currently selected area. Selection ATof disulphide bridges is identical to normal bonds, and may be adjusted ATusing the RasMol AXsetbondmode set bondmode ATcommand. The colour of disulphide bonds may be changed using the AXcolour colour ssbonds ATcommand. By default, each disulphide bond has the colours of its connected ATatoms. AP ATBy default disulphide bonds are drawn between the sulphur atoms within ATthe cysteine groups. By using the AXsetssbonds set ssbonds ATcommand the position of the cysteine's alpha carbons may be used instead. AB ASStructure NRSyntax: structure NR HR<pre> HRSyntax: structure HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRstructure\par RR}\pard\par ATThe RasMol ACstructure ATcommand calculates secondary structure assignments ATfor the currently loaded protein. If the original PDB file contained ATstructural assignment records (HELIX and SHEET) these are discarded. ATInitially, the hydrogen bonds of the current molecule are found, if this AThasn't been done already. The secondary structure is the determined using ATKabsch and Sander's DSSP algorithm. Once finished the program reports the ATnumber of helices and ladders found. AB ASTranslate NRSyntax: translate <axis> {-} <value> NR HR<pre> HRSyntax: translate <axis> {-} <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRtranslate <axis> \{-\} <value>\par RR}\pard\par ATThe RasMol ACtranslate ATcommand moves the position of the centre of the molecule on the ATscreen. The axis parameter specifies along which axis the molecule ATis to be moved and the integer parameter specifies the absolute ATposition of the molecule centre from the middle of the screen. ATPermited values for the axis parameter are HT"<tt><b>x</b></tt>", "<tt><b>y</b></tt>" and "<tt><b>z</b></tt>". RT"{\f2\b x}", "{\f2\b y}" and "{\f2\b z}". MT"x", "y" and "z". NT"x", "y" and "z". ATDisplacement values must be between -100 and 100 which correspond to ATmoving the current molecule just off the screen. A positive HT"<tt><b>x</b></tt>" RT"{\f2\b x}" MT"x" NT"x" ATdisplacement moves the molecule to the right, and a positive HT"<tt><b>y</b></tt>" RT"{\f2\b y}" MT"y" NT"y" ATdisplacement moves the molecule down the screen. The pair of commands ACtranslate x 0 ATand ACtranslate y 0 ATcentres the molecule on the screen. AB ASWireframe NRSyntax: wireframe {<boolean>} NR wireframe <value> NR HR<pre> HRSyntax: wireframe {<boolean>} HR wireframe <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRwireframe \{<boolean>\}\line\tab RRwireframe <value>\par RR}\pard\par ATRepresent each bond within the selected zone of the molecule as either ATa cylinder or depth-cued vector. If no parameter is given, RasMol draws ATeach bond as a hither-and-yon shaded narrow vector. An integer parameter ATspecifies the radius of a cylinder, given in 4nm units, to be used as a ATstick bond. AB ASWrite NRSyntax: write {<format>} <filename> NR HR<pre> HRSyntax: write {<format>} <filename> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRwrite \{<format>\} <filename>\par RR}\pard\par ATWrite the current image to a file in a standard raster format. Currently ATsupported file formats include AC"gif AT(Compuserve GIF), AC"ppm AT(Portable Pixmap), AC"ras AT(Sun rasterfile), AC"ps ATand AC"epsf AT(Encapsulated PostScript), AC"monops AT(Monochrome Encapsulated PostScript) and AC"bmp AT(Microsoft bitmap). This command should not be confused with the RasMol AXsave save ATcommand which save the currently selected portion of the molecule. AB ASZap NRSyntax: zap NR HR<pre> HRSyntax: zap HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRzap\par RR}\pard\par ATDeletes the contents of the current database and resets parameter ATvariables to their initial default state. AB ASZoom NRSyntax: zoom {<boolean>} NR zoom <value> NR HR<pre> HRSyntax: zoom {<boolean>} HR zoom <value> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRzoom \{<boolean>\}\line\tab RRzoom <value>\par RR}\pard\par ATChange the magnification of the currently displayed image. Boolean ATparameters either magnify or reset the scale of current molecule. An ATinteger parameter between 10 and 200 specifies the desired magnification ATas a percentage of the default scale. AB TR INTERNAL PARAMETERS TR =================== TR PR?parameters PR?set parameters PR?internal parameters PRInternal Parameters RR#{\footnote chsetopt} RR${\footnote Internal Parameters} RR{\fs24\b Internal Parameters}\par\par MR.SH SET PARAMETERS HR<a name="chsetopt"><h2>Internal Parameters</h2></a> ATRasMol has a number of internal parameters that may be modified using the AXset set ATcommand. These parameters control a number of program options such as ATrendering options and mouse button mappings. AP PTA complete list of internal parameter names is given below. Type "help PTset <parametername>" for more information on each option. PP HTA complete list of internal parameter names is given below. HP RTA complete list of internal parameter names is given below. RP PR ambient background bondmode display PR hbond hetero hourglass hydrogen PR mouse ribbons shadow slabmode PR specular specpower ssbonds strands HR<pre> HR <a href="#setambient">Ambient</a HR> <a href="#setbackground">Background</a HR> <a href="#setbondmode">BondMode</a> HR <a href="#sethbonds">HBonds</a HR> <a href="#sethetero">Hetero</a HR> <a href="#sethourglass">HourGlass</a> HR <a href="#sethydrogen">Hydrogen</a HR> <a href="#setmouse">Mouse</a HR> <a href="#setshadow">Shadow</a> HR <a href="#setslabmode">SlabMode</a HR> <a href="#setspecular">Specular</a HR> <a href="#setspecpower">SpecPower</a> HR <a href="#setssbonds">SSBonds</a HR> <a href="#setstrands">Strands</a> HR</pre> RR\cellx1200\cellx2400\cellx3600\cellx4800 RR\intbl RR{\uldb ambient}{\v setambient}\cell RR{\uldb background}{\v setbackground}\cell RR{\uldb bondmode}{\v setbondmode}\cell RR{\uldb hbonds}{\v sethbonds}\cell RR\row\intbl RR{\uldb hetero}{\v sethetero}\cell RR{\uldb hourglass}{\v sethourglass}\cell RR{\uldb hydrogen}{\v sethydrogen}\cell RR{\uldb mouse}{\v setmouse}\cell RR\row\intbl RR{\uldb shadow}{\v setshadow}\cell RR{\uldb slabmode}{\v setslabmode}\cell RR{\uldb specular}{\v setspecular}\cell RR{\uldb specpower}{\v setspecpower}\cell RR\row\intbl RR{\uldb ssbonds}{\v setssbonds}\cell RR{\uldb strands}{\v setstrands}\cell RR\row\pard\par AB PR?ambient ASSet Ambient RRK{\footnote ambient} NRSyntax: set ambient {<value>} NR HR<pre> HRSyntax: set ambient {<value>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset ambient \{<value>\}\par RR}\pard\par ATThe RasMol ACambient ATparameter is used to control the amount of ambient (or surrounding) ATlight in the scene. The ACambient ATvalue must be between 0 and 100 that controls the percentage intensity ATof the darkest shade of an object. For a solid object, this is the ATintensity of surfaces facing away from the light source or in shadow. ATFor depth-cued objects this is the intensity of objects furthest from ATthe viewer. AP ATThis parameter is commonly used to correct for monitors with different AT"gamma values" (brightness), to change how light or dark a hardcopy ATimage appears when printed or to alter the feeling of depth for ATwireframe or ribbon representations. AB ASSet Background RRK{\footnote background} NRSyntax: set background <colour> NR HR<pre> HRSyntax: set background {<colour>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset background <colour>\par RR}\pard\par ATThe RasMol ACbackground ATparameter is used to set the colour of the "canvas" background. The ATcolour may be given as either a colour name or a comma separated ATtriple of Red, Green, Blue (RGB) components enclosed in square ATbrackets. Typing the command AXhelp help colours ATwill give a list of the predefined colour names recognised by RasMol. ATWhen running under X Windows, RasMol also recognises colours in the ATX server's colour name database. AB PR?bondmode ASSet BondMode RRK{\footnote bondmode} NRSyntax: set bondmode and NR set bondmode or NR HR<pre> HRSyntax: set bondmode and HR set bondmode or HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset bondmode and\line\tab RRset bondmode or\par RR}\pard\par ATset bondmode AB ASSet Display RRK{\footnote display} NRSyntax: set display selected NR set display normal NR HR<pre> HRSyntax: set display selected HR set display normal HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset display selected\line\tab RRset display normal\par RR}\pard\par ATset display AB ASSet HBonds RRK{\footnote hbonds} RRK{\footnote sidechain} RRK{\footnote backbone} NRSyntax: set hbonds backbone NR set hbonds sidechain NR HR<pre> HRSyntax: set hbonds backbone HR set hbonds sidechain HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset hbonds backbone\line\tab RRset hbonds sidechain\par RR}\pard\par ATset hbonds AB ASSet Hetero RRK{\footnote hetero} NRSyntax: set hetero <boolean> NR HR<pre> HRSyntax: set hetero <boolean> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset hetero <boolean>\par RR}\pard\par ATset hetero AB ASSet HourGlass RRK{\footnote hourglass} NRSyntax: set hourglass <boolean> NR HR<pre> HRSyntax: set hourglass <boolean> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset hourglass \{<boolean>\}\par RR}\pard\par ATThe RasMol AChourglass ATparameter allows the user to enable and disable the use of the `hour ATglass' cursor used by RasMol to indicate that the program is currently ATbusy drawing the next frame. The command ACset hourglass on ATenable the indicator, whilst ACset hourglass off ATprevents RasMol from changing the cursor. This is useful when spinning ATthe molecule, running a sequence of commands from a script file or ATusing interprocess communication to execute complex sequences of ATcommands. In these cases a `flashing' cursor may be distracting. AB ASSet Hydrogen RRK{\footnote hydrogen} NRSyntax: set hydrogen <boolean> NR HR<pre> HRSyntax: set hydrogen <boolean> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset hydrogen <boolean>\par RR}\pard\par ATset hydrogen AB ASSet Mouse RRK{\footnote mouse} RRK{\footnote rasmol} RRK{\footnote insight} RRK{\footnote quanta} NRSyntax: set mouse rasmol NR set mouse insight NR set mouse quanta NR HR<pre> HRSyntax: set mouse rasmol HR set mouse insight HR set mouse quanta HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset mouse rasmol\line\tab RRset mouse insight\line\tab RRset mouse quanta\par RR}\pard\par ATThe RasMol ACset mouse ATcommand sets the rotation, translation, scaling and zooming mouse ATbindings. The default value is ACrasmol ATwhich is suitable for two button mice (for three button mice the ATsecond and third buttons are synonymous); X-Y rotation is controlled ATby the first button, and X-Y translation by the second. Additional ATfunctions are controlled by holding a modifier key on the keyboard. AT[Shift] and the first button performs scaling, [shift] and the second ATbutton performs Z-rotation, and [control] and the first mouse button ATcontrols the clipping plane. The ACinsight ATand ACquanta ATprovide the same mouse bindings as other packages for experienced ATusers. AB ASSet Ribbons RRK{\footnote ribbons} RRK{\footnote strands} RRK{\footnote solid} NRSyntax: set ribbons strands NR set ribbons solid NR HR<pre> HRSyntax: set ribbons strands HR set ribbons solid HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset ribbons strands\line\tab RRset ribbons solid\par RR}\pard\par ATThe RasMol ACset ribbons ATcommand controls the way that macromolecular ribbons are displayed. ATThe default value ACstrands ATdisplay macromolecular ribbons as parallel depth-cued strands that ATpass along the protein or nucleic acid backbone. The number of strands ATin the ribbon may be altered using the RasMol AXsetstrands set strands ATcommand. The ACset ribbons solid ATcommand renders the macromolecular ribbon as a solid shaded ribbon. AB ASSet Shadow RRK{\footnote shadow} NRSyntax: set shadow <boolean> NR HR<pre> HRSyntax: set shadow <boolean> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset shadow <boolean>\par RR}\pard\par ATThe RasMol ACset shadow ATcommand enables and disables raytracing of the currently rendered image. ATCurrently only the spacefilling representation is shadowed or can cast ATshadows. Enabling shadowing will automatically disable the Z-clipping AT(slabbing) plane using the command AXslab slab off. ATRaytracing typically takes about 10s for a moderately sized protein. ATIt is recommended that shadowing is normally disabled whilst the ATmolecule is being transformed or manipulated, and only enabled once ATan appropiate viewpoint is selected, to provide a greater impression ATof depth. AB ASSet SlabMode RRK{\footnote slabmode} RRK{\footnote reject} RRK{\footnote half} RRK{\footnote hollow} RRK{\footnote solid} RRK{\footnote section} NRSyntax: set slabmode <slabmode> NR HR<pre> HRSyntax: set slabmode <slabmode> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset slabmode <slabmode>\par RR}\pard\par ATThe RasMol ACslabmode ATparameter controls the rendering method of objects cut by the ATslabbing (z-clipping) plane. Valid slab modes are HT"<tt><b>reject</b></tt>", "<tt><b>half</b></tt>", HT"<tt><b>hollow</b></tt>", "<tt><b>solid</b></tt>" and HT"<tt><b>section</b></tt>". RT"{\f2\b reject}", "{\f2\b half}", "{\f2\b hollow}", RT"{\f2\b solid}" and "{\f2\b section}". NT"reject", "half", "hollow", "solid" and "section". MT"reject", "half", "hollow", "solid" and "section". AB ASSet Specular RRK{\footnote specular} NRSyntax: set specular <boolean> NR HR<pre> HRSyntax: set specular <boolean> HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset specular <boolean>\par RR}\pard\par ATThe RasMol ACset specular ATcommand enables and disables the display of specular highlights on ATsolid objects drawn by RasMol. Specular highlights appear as white ATreflections of the light source on the surface of the object. The ATcurrent RasMol implementation uses an approximation function to ATgenerate this highlight. AP ATThe specular highlights on the surfaces of solid objects may be ATaltered by using the specular reflection coefficient, which is ATaltered using the RasMol AXsetspecpower set specpower ATcommand. AB ASSet SpecPower RRK{\footnote specpower} NRSyntax: set specpower {<value>} NR HR<pre> HRSyntax: set specpower {<value>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset specpower \{<value>\}\par RR}\pard\par ATThe ACspecpower ATparameter determines the shininess of solid objects rendered by ATRasMol. This value between 0 and 100 adjusts the reflection ATcoeffient used in specular highlight calculations. The specular AThighlights are enabled and disabled by the RasMol AXsetspecular set specular ATcommand. Values around 20 or 30 produce plastic looking surfaces. ATHigh values represent more shiny surfaces such as metals, while ATlower values produce more diffuse/dull surfaces. AB ASSet SSBonds RRK{\footnote ssbonds} RRK{\footnote backbone} RRK{\footnote sidechain} NRSyntax: set ssbonds backbone NR set ssbonds sidechain NR HR<pre> HRSyntax: set ssbonds backbone HR set ssbonds sidechain HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset ssbonds backbone\line\tab RRset ssbonds sidechain\par RR}\pard\par ATset ssbonds AB ASSet Strands RRK{\footnote strands} NRSyntax: set strands {<value>} NR HR<pre> HRSyntax: set strands {<value>} HR</pre><p> RR\tx1200 RR{\f2\b Syntax:\tab RRset strands \{<value>\}\par RR}\pard\par ATThe RasMol ACstrands ATparameter controls the number of parallel strands that are displayed ATin the ribbon representations of proteins. The permissible values for ATthis parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The ATnumber of strands is constant for all ribbons being displayed. ATHowever, the ribbon width (the separation between strands) may be ATcontrolled on a residue by residue basis using the RasMol AXribbons ribbons ATcommand. AB TR ATOM EXPRESSIONS TR ================ TR PR?expression PR?expressions PR?atom expressions PRAtom Expressions RR#{\footnote chexprs} RR${\footnote Atom Expressions} RR{\fs24\b Atom Expressions}\par\par MR.SH ATOM EXPRESSIONS HR<a name="chexprs"><h2>Atom Expressions</h2></a> ATRasMol atom expressions uniquely identify an arbitrary group of atoms ATwithin a molecule. Atom expressions are composed of either primitive ATexpressions, PT(for more details type "help primitives"), ATpredefined sets, PT(type "help sets"), ATcomparison operators, PT("help comparisons"), ACwithin ATexpressions, PT("help within") ATor logical (boolean) combinations of the above expression types. AP ATThe logical operators allow complex queries to be constructed out of ATsimpler ones using the standard boolean connectives ACand, or ATand ACnot. ATThese may be abbreviated by the symbols HT"<tt>&</tt>", "<tt>|</tt>" and "<tt>!</tt>" RT"{\f2\b &}", "{\f2\b |}" and "{\f2\b !}" MT"&", "|" and "!" NT"&", "|" and "!" ATrespectively. Parentheses (brackets) may be used to alter the ATprecedence of the operators. For convenience, a comma may also ATbe used for boolean disjunction. AP ATThe atom expression is evaluated for each atom, hence ACprotein and backbone ATselects protein bacbone atoms, not the protein and [nucleic] acid ATbackbone atoms! AP PRExamples: backbone and not helix PR within( 800, ser70 ) PR not (hydrogen or hetero) PR not *.FE and hetero PR 8, 12, 16, 20-28 PR arg, his, lys HR<ul> HR<li><a href="#primitiveexpressions">Primitive Expressions</a> HR<li><a href="#predefinedsets">Predefined Sets</a> HR<li><a href="#comparisonoperators">Comparison Operators</a> HR<li><a href="#withinexpressions"><tt>Within</tt> Expressions</a> HR<p><li><a href="#exampleexpressions">Examples</a> HR</ul> RR\tx250\li250\fi-250 RR{\f1\'b7}\tab RR{\uldb Primitive Expressions}{\v primitiveexpressions}\par RR{\f1\'b7}\tab RR{\uldb Predefined Sets}{\v predefinedsets}\par RR{\f1\'b7}\tab RR{\uldb Comparison Operators}{\v comparisonoperators}\par RR{\f1\'b7}\tab RR{\uldb Within Expressions}{\v withinexpressions}\par\par RR{\f1\'b7}\tab RR{\uldb Example Expressions}{\v exampleexpressions}\par RR\pard AB ASExample Expressions ATThe following table gives some useful examples of RasMol ATatom expressions. PTFor examples of the precise syntax, type "help expressions". AP PR Expression Interpretation PR PR * All atoms PR cys Atoms in cysteines PR hoh Atoms in heterogenous water molecules PR as? Atoms in either asparagine or aspartic acid PR *120 Atoms at residue 120 of all chains PR *p Atoms in chain P PR *.n? Nitrogen atoms PR cys.sg Sulphur atoms in cysteine residues PR ser70.c? Carbon atoms in serine-70 PR hem*p.fe Iron atoms in the Heme groups of chain P HR<pre> HR <b>Expression</b> <b>Interpretation</b> HR HR * All atoms HR cys Atoms in cysteines HR hoh Atoms in heterogenous water molecules HR as? Atoms in either asparagine or aspartic acid HR *120 Atoms at residue 120 of all chains HR *p Atoms in chain P HR *.n? Nitrogen atoms HR cys.sg Sulphur atoms in cysteine residues HR ser70.c? Carbon atoms in serine-70 HR hem*p.fe Iron atoms in the Heme groups of chain P HR</pre> RR\tx1500\li1500\fi-1250 RR{\b Expression} RR\tab{\b Interpretation}\line\par RR{\f2\b *} RR\tab All atoms\par RR{\f2\b cys} RR\tab Atoms in cysteines\par RR{\f2\b hoh} RR\tab Atoms in heterogenous water molecules\par RR{\f2\b as?} RR\tab Atoms in either asparagine or aspartic acid\par RR{\f2\b *120} RR\tab Atoms at residue 120 of all chains\par RR{\f2\b *p} RR\tab Atoms in chain P\par RR{\f2\b *.n?} RR\tab Nitrogen atoms\par RR{\f2\b cys.sg} RR\tab Sulphur atoms in cysteine residues\par RR{\f2\b ser70.c?} RR\tab Carbon atoms in serine-70\par RR{\f2\b hem*p.fe} RR\tab Iron atoms in the Heme groups of chain P\par RR\par\pard AB ASPrimitive Expressions ATRasMol primitive expressions are the fundamental building blocks ATof atom expressions. There a two basic types of primitive expression. ATThe first type is used to identify a given residue number or range ATof residue numbers. A single residue is identified by its number AT(position in the sequence), and a range is specified by lower and ATupper bounds separated by a hyphen character. For example ACselect 5,6,7,8 ATis also ACselect 5-8. ATNote that this selects the given residue numbers in all macromolecule ATchains. AP ATThe second type of primitive expression specifies a sequence of fields ATthat must match for a given atom. The first part specifies a residue AT(or group of residues) and an optional second part specifies the atoms ATwithin those residues. The first part consists of a residue name, AToptionally followed by a residue number and/or chain identifier. VP VTA residue name typically consists of up to three alphabetic characters, VTwhich are case insensitive. Hence the primitive expressions VCSER VTand VCser VTare equivalent, identifying all cysteine residues. VTResidue names that contain non-alphabetic characters, such as VTsulphate groups, may be delimited using square brackets, i.e. VC[SO4] VP VTThe residue number is the residue's position in the macromolecule VTsequence. Negative sequence numbers are permited. For example, VCSER70 VTCare must be taken when specifying both residue name and number, VTit the group at the specified position isn't the specified residue VTno atoms are selected. VP VTThe chain identifier is typically a single case-insensitive VTalphabetic or numeric character. Numeric chain identifiers must VTbe distinguished or separated from residue numbers by a colon VTcharacter. For example, VCSER70A VTor VCSER70:1 VP ATThe second part consists of a period character followed by an atom ATname. VTAn atom name may be up to four alphabetic or numeric characters. VP ATAn asterisk may be used as a wild card for a whole field and a ATquestion mark as a single character wildcard. PP PTFor examples of RasMol expressions type "help examples". AB PR?comparison PR?comparisons PR?comparison expressions ASComparison Operators ATParts of a molecule may also be distinguished using equality, ATinequality and ordering operators on their properties. The format ATof such comparison expression is a property name, followed by a ATcomparison operator and then an integer value. AP ATThe atom properties that may be used in RasMol are ACatomno ATfor the atom serial number, ACresno ATfor the residue number, ACradius ATfor the spacefill radius in RasMol units (or zero if not represented ATas a sphere) and ACtemperature ATfor the PDB anisotropic temperature value. AP ATThe equality operator is denoted either RT"{\f2\b =}" or "{\f2\b ==}". HT"<tt><b>=</b></tt>" or "<tt><b>==</b></tt>". NT"=" or "==". MT"=" or "==". ATThe inequality operator as either RT"{\f2\b <>}", "{\f2\b !=}" or "{\f2\b /=}". HT"<tt><b><></b></tt>", "<tt><b>!=</b></tt>" or HT"<tt><b>/=</b></tt>". NT"<>", "!=" or "/=". MT"<>", "!=" or "/=". ATThe ordering operators are RT"{\f2\b <}" HT"<tt><b><</b></tt>" NT"<" MT"<" ATfor less than, RT"{\f2\b <=}" HT"<tt><b><=</b></tt>" NT"<=" MT"<=" ATfor less than or equal to, RT"{\f2\b >}" HT"<tt><b>></b></tt>" NT">" MT">" ATfor greater than, and RT"{\f2\b >=}" HT"<tt><b>>=</b></tt>" NT">" MT">" ATfor greater than or equal to. AP PRExamples: resno < 23 PR temperature >= 900 PR atomno == 487 HR<pre> HRExamples: resno < 23 HR temperature >= 900 HR atomno == 487 HR</pre> RR\tx1500 RR{\f2\b Examples: RR\tab resno < 23\par RR\tab temperature >= 900\par RR\tab atomno == 487\par RR}\pard\par AB ASWithin Expressions RRK{\footnote within} ATA RasMol ACwithin ATexpression allows atoms to be selected on their proximity to ATanother set of atoms. A ACwithin ATexpression takes two parameters separated by a comma and surrounded ATby parenthesis. The first argument is an integer value called the AT"cut-off" distance of the within expression and the second argument ATis any valid atom expression. The cut-off distance is expressed in ATRasMol 0.004 Angstrom units. An atom is selected if it is within ATthe cut-off distance of any of the atoms defined by the second ATargument. This allows complex expressions to be constructed containing ATnested ACwithin ATexpressions. AP ATFor example, the command ACselect within(800,backbone) ATselects any atom within a 3.2 Angstrom radius of any atom in a ATprotein or nucleic acid backbone. ACWithin ATexpressions are particularly usefull for selecting the atoms ATaround an active site. AB PR?sets ASPredefined Sets RRK{\footnote sets} ATRasMol atom expressions may contain predefined sets. Thsese sets ATare single keywords that represent portions of a molecule of interest. ATPredefined sets are often abbreviations primitive atom expressions, ATand in some cases of selecting areas of a molecule that could not ATotherwise be distinguished. A list of the currently predfined sets ATis given below. PTType "help sets setname" for more information about a given set. AP PR at acidic acyclic aliphatic PR alpha amino aromatic backbone PR basic buried cg charged PR cyclic cystine helix hetero PR hydrogen hydrophobic large medium PR neutral nucleic polar protein PR purine pyrimidine selected sheet PR sidechain small surface turn PR water HR<pre> HR <a href="#atset">AT</a HR> <a href="#acidicset">Acidic</a HR> <a href="#acyclicset">Acyclic</a> HR <a href="#aliphaticset">Aliphatic</a HR> <a href="#alphaset">Alpha</a HR> <a href="#aminoset">Amino</a> HR <a href="#aromaticset">Aromatic</a HR> <a href="#backboneset">Backbone</a HR> <a href="#basicset">Basic</a> HR <a href="#buriedset">Buried</a HR> <a href="#cgset">CG</a HR> <a href="#chargedset">Charged</a> HR <a href="#cyclicset">Cyclic</a HR> <a href="#cystineset">Cystine</a HR> <a href="#helixset">Helix</a> HR <a href="#heteroset">Hetero</a HR> <a href="#hydrogenset">Hydrogen</a HR> <a href="#hydrophobicset">Hydrophobic</a> HR <a href="#largeset">Large</a HR> <a href="#mediumset">Medium</a HR> <a href="#neutralset">Neutral</a> HR <a href="#nucleicset">Nucleic</a HR> <a href="#polarset">Polar</a HR> <a href="#proteinset">Protein</a> HR <a href="#purineset">Purine</a HR> <a href="#pyrimidineset">Pyrimidine</a HR> <a href="#selectedset">Selected</a> HR <a href="#sheetset">Sheet</a HR> <a href="#sidechainset">Sidechain</a HR> <a href="#smallset">Small</a> HR <a href="#surfaceset">Surface</a HR> <a href="#turnset">Turn</a HR> <a href="#waterset">Water</a> HR</pre> RR\cellx1200\cellx2400\cellx3600\cellx4800 RR\intbl RR{\uldb at}{\v atset}\cell RR{\uldb acidic}{\v acidicset}\cell RR{\uldb acyclic}{\v acyclicset}\cell RR{\uldb aliphatic}{\v aliphaticset}\cell RR\row\intbl RR{\uldb alpha}{\v alphaset}\cell RR{\uldb amino}{\v aminoset}\cell RR{\uldb aromatic}{\v aromaticset}\cell RR{\uldb backbone}{\v backboneset}\cell RR\row\intbl RR{\uldb basic}{\v basicset}\cell RR{\uldb buried}{\v buriedset}\cell RR{\uldb cg}{\v cgset}\cell RR{\uldb charged}{\v chargedset}\cell RR\row\intbl RR{\uldb cyclic}{\v cyclicset}\cell RR{\uldb cystine}{\v cystineset}\cell RR{\uldb helix}{\v helixset}\cell RR{\uldb hetero}{\v heteroset}\cell RR\row\intbl RR{\uldb hydrogen}{\v hydrogenset}\cell RR{\uldb hydrophobic}{\v hydrophobicset}\cell RR{\uldb large}{\v largeset}\cell RR{\uldb medium}{\v mediumset}\cell RR\row\intbl RR{\uldb neutral}{\v neutralset}\cell RR{\uldb nucleic}{\v nucleicset}\cell RR{\uldb polar}{\v polarset}\cell RR{\uldb protein}{\v proteinset}\cell RR\row\intbl RR{\uldb purine}{\v purineset}\cell RR{\uldb pyrimidine}{\v pyrimidineset}\cell RR{\uldb selected}{\v selectedset}\cell RR{\uldb sheet}{\v sheetset}\cell RR\row\intbl RR{\uldb sidechain}{\v sidechainset}\cell RR{\uldb small}{\v smallset}\cell RR{\uldb surface}{\v surfaceset}\cell RR{\uldb turn}{\v turnset}\cell RR\row\intbl RR{\uldb water}{\v waterset}\cell RR\row\pard\par AB MR.SH Predefined Sets ASAT Set RRK{\footnote at} ATThis set contains the atoms in the complementary nucleotides ATadenosine and thymidine (A and T respectively). All nucleotides ATare classified as either the set ACat ATor the set AXcgset cg ATThis set is equivalent to the RasMol atom expressions AC"a,t ATand AC"nucleic and not cg AB ASAcidic Set RRK{\footnote acidic} ATThe set of acidic amino acids. ATThese are the residue types Asp, Glu and Tyr. ATAll amino acids are classified as either ACacidic, AXbasicset basic ACor AXneutralset neutral. ATThis set is equivalent to the RasMol atom expressions AC"asp, glu, tyr ATand AC"amino and not (basic or neutral) AB ASAcyclic Set RRK{\footnote acyclic} ATThe set of atoms in amino acids not containing a cycle or ATring. All amino acids are classified as either AXcyclicset cyclic ATor ACacyclic. ATThis set is equivalent to the RasMol atom expression AC"amino and not cyclic AB ASAliphatic Set RRK{\footnote aliphatic} ATThis set contains the aliphatic amino acids. ATThese are the amino acids Ala, Gly, Ile, Leu and Val. ATThis set is equiavlent to the RasMol atom expression AC"ala, gly, ile, leu, val AB ASAlpha Set RRK{\footnote alpha} ATThe set of alpha carbons in the protein molecule. This set is ATapproximately equivalent to the RasMol atom expression AC"*.CA ATThis command should not be confused with the predefined set AXhelixset helix ATwhich contains the atoms in the amino acids of the protein's ATalpha helices. AB ASAmino Set RRK{\footnote amino} ATThis set contains all the atoms contained in amino acid residues. ATThis is useful for distinguishing the protein from the nucleic ATacid and heterogenous atoms in the current molecule database. AB ASAromatic Set RRK{\footnote aromatic} ATThe set of atoms in amino acids containing aromatic rings. ATThese are the amino acids His, Phe, Trp and Tyr. ATBecause they contain aromatic rings all members of this ATset are member of the predefined set AXcyclicset cyclic. ATThis set is equivalent to the RasMol atom expressions AC"his, phe, trp, tyr ATand AC"cyclic and not pro AB ASBackbone Set RRK{\footnote backbone} ATThis set contains the four atoms of each amino acid that form the ATpolypeptide N-C-C-O backbone of proteins, and the atoms the sugar ATphosphate backbone of nucleic acids. ATUse the RasMol predefined sets ACprotein ATand ACnucleic ATto distinguish between the two forms of backbone. ATAtoms in nucleic acids and proteins are either ACbackbone ATor AXsidechainset sidechain. ATThis set is equivalent to the RasMol expression AT"(protein or nucleic) and not sidechain AB ASBasic Set RRK{\footnote basic} ATThe set of basic amino acids. ATThese are the residue types Asp, Glu and Tyr. ATAll amino acids are classified as either AXacidicset acidic, ACbasic ATor AXneutralset neutral. ATThis set is equivalent to the RasMol atom expressions AC"asp, glu, tyr ATand AC"amino and not (acidic or neutral) AB ASBuried Set RRK{\footnote buried} ATThis set contains the atoms in those amino acids that tend AT(prefer) to buried inside protein, away from contact with ATsolvent molecules. This set refers to the amino acids ATpreference and not the actual solvent acessibility for ATthe current protein. ATAll amino acids are classified as either AXsurfaceset surface ATor ACburied. ATThis set is equivalent to the RasMol atom expression AC"amino and not surface AB ASCG Set RRK{\footnote cg} ATThis set contains the atoms in the complementary nucleotides ATcytidine and guanoine (C and G respectively). All nucleotides ATare classified as either the set AXatset at ATor the set ACcg ATThis set is equivalent to the RasMol atom expressions AC"c,g ATand AC"nucleic and not at AB ASCharged Set RRK{\footnote charged} ATThis set contains the charged amino acids. These are the amino ATacids that are either AXacidicset acidic ATor AXbasicset basic. ATAmino acids are classified as being either ACcharged ATor AXneutralset neutral. ATThis set is equivalent to the RasMol atom expressions AC"acidic or basic ATand AC"amino and not neutral AB ASCyclic Set RRK{\footnote cyclic} ATThe set of atoms in amino acids containing a cycle or rings. ATAll amino acids are classified as either ACcyclic ATor AXacyclicset acyclic. ATThis set consists of the amino acids His, Phe, Pro, Trp and Tyr. ATThe members of the predefined set AXaromaticset aromatic ATare members of this set. ATThe only cyclic but non-aromatic amino acid is proline. ATThis set is equivalent to the RasMol atom expressions AC"his, phe, pro, trp, tyr ATand AC"aromatic or pro ATand AC"amino and not acyclic AB ASCystine Set RRK{\footnote cystine} ATThis set contains the atoms of cysteine residues that form part ATof a disulphide bridge, i.e. half cystines. RasMol automatically ATdetermines disulphide bridges, if neither the predefined set ACcystine ATnor the RasMol AXssbonds ssbonds ATcommand have been used since the molecule was loaded. The set of ATfree cysteines may be determined using the RasMol atom expression AC"cys and not cystine AB ASHelix Set RRK{\footnote helix} ATThis set contains all atoms that form part of a protein alpha AThelix as determined by either the PDB file author or Kabsch and ATSander's DSSP algorithm. By default, RasMol uses the secondary ATstructure determination given in the PDB file if it exists. ATOtherwise, it uses the DSSP algorithm as used by the RasMol AXstructure structure ATcommand. AP ATThis command should not be confused with the predefined set AXalphaset alpha ATwhich contains the alpha carbon atoms of a protein. AB ASHetero Set RRK{\footnote hetero} ATThis set contains all the heterogenous atoms in the molecule. These ATare the atoms described by HETATM entries in the PDB file. These ATtypically contain water, cofactors and other solvents and ligands. ATThe RasMol predefined set AXwaterset water ATis often used to partition this set. AB ASHydrogen Set RRK{\footnote hydrogen} ATThis predefined set contains all the hydrogen and deuterium atoms ATof the current molecule. AB ASHydrophobic Set RRK{\footnote hydrophobic} ATThis set contains all the hydrophobic amino acids. ATThese are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. ATAll amino acids are classified as either AChydrophobic ATor AXpolarset polar. ATThis set is equivalent to the RasMol atom expressions AC"ala, leu, val, ile, pro, phe, met, trp ATand AC"amino and not polar AB ASLarge Set RRK{\footnote large} ATAll amino acids are classified as either AXsmallset small, AXmediumset medium ATor AClarge. ATThis set is equivalent to the RasMol atom expression AC"amino and not (small or medium) AB ASMedium Set RRK{\footnote medium} ATAll amino acids are classified as either AXsmallset small, ACmedium ATor AXlargeset large. ATThis set is equivalent to the RasMol atom expression AC"amino and not (large or small) AB ASNeutral Set RRK{\footnote neutral} ATThe set of neutral amino acids. ATAll amino acids are classified as either AXacidicset acidic, ACbasic ACor AXneutralset neutral. ATThis set is equivalent to the RasMol atom expression AC"amino and not (acidic or basic) AB ASNucleic Set RRK{\footnote nucleic} ATThe set of all atoms in nucleic acids. AB ASPolar Set RRK{\footnote polar} ATThis set contains the polar amino acids. ATAll amino acids are classified as either AXhydrophobicset hydrophobic ATor ACpolar. ATThis set is equivalent to the RasMol atom expression AC"amino and not hydrophobic AB ASProtein Set RRK{\footnote protein} ATThe set of all atoms in proteins. This consists of the RasMol ATpredefined set AXaminoset amino ATand common post-translation modifications. AB ASPurine Set RRK{\footnote purine} ATThe set of purine nucleotides. ATThese are the bases adenosine and guanosine (A and G respectively). ATAll nucleotides are either ACpurines ATor AXpyrimidineset pyrimidines. ATThis set is equivalent to the RasMol atom expressions AC"a,g ATand AC"nucleic and not purine AB ASPyrimidine Set RRK{\footnote pyrimidine} ATThe set of pyrimidine nucleotides. ATThese are the bases cytidine and thymidine (C and T respectively). ATAll nucleotides are either ACpurineset purines ATor ACpyrimidines. ATThis set is equivalent to the RasMol atom expressions AC"c,t ATand AC"nucleic and not pyrimidine AB ASSelected Set RRK{\footnote selected} ATThis set contains the set of atoms in the currently active zone. ATThe currently active zone is defined by the preceding AXselect select ATor AXrestrict restrict ATcommand and not the atom expression containing the ACselected ATkeyword. AB ASSheet Set RRK{\footnote sheet} ATThis set contains all atoms that form part of a protein beta ATsheet as determined by either the PDB file author or Kabsch and ATSander's DSSP algorithm. By default, RasMol uses the secondary ATstructure determination given in the PDB file if it exists. ATOtherwise, it uses the DSSP algorithm as used by the RasMol AXstructure structure ATcommand. AB ASSidechain Set RRK{\footnote sidechain} ATThis set contains the functional sidechains of any amino acids ATand the base of each nucleotide. These are the atoms not part of ATthe polypeptide N-C-C-O backbone of proteins or the sugar ATphosphate backbone of nucleic acids. ATUse the RasMol predefined sets ACprotein ATand ACnucleic ATto distinguish between the two forms of sidechain. ATAtoms in nucleic acids and proteins are either AXbackboneset backbone ATor ACsidechain. ATThis set is equivalent to the RasMol expression AT"(protein or nucleic) and not backbone AB ASSmall Set RRK{\footnote small} ATAll amino acids are classified as either ACsmall, AXmediumset medium ATor AXlargeset large. ATThis set is equivalent to the RasMol atom expression AC"amino and not (medium or large) AB ASSurface Set RRK{\footnote surface} ATThis set contains the atoms in those amino acids that tend AT(prefer) to be on the surface of proteins, in contact with ATsolvent molecules. This set refers to the amino acids ATpreference and not the actual solvent acessibility for ATthe current protein. ATAll amino acids are classified as either ACsurface ATor AXburiedset buried. ATThis set is equivalent to the RasMol atom expression AC"amino and not buried AB ASTurn Set RRK{\footnote turn} ATThis set contains all atoms that form part of a protein turns ATas determined by either the PDB file author or Kabsch and ATSander's DSSP algorithm. By default, RasMol uses the secondary ATstructure determination given in the PDB file if it exists. ATOtherwise, it uses the DSSP algorithm as used by the RasMol AXstructure structure ATcommand. AB ASWater Set RRK{\footnote water} ATThis set contains all the heterogenous water molecules in the current ATdatabase. A large number of water molecules are sometimes associated ATwith protein and nucleic acid structures determined by X-ray ATcrystallography. These atoms tend to clutter an image. AB TR Colour Schemes TR ============== TR PR?colors PR?colours PR?color schemes PR?colour schemes PR?color names PR?colour names PR?predefined colors PR?predefined colours PRColour Schemes RR#{\footnote chcolours} RR${\footnote Colour Schemes} RR{\fs24\b Colour Schemes}\par\par MR.SH COLOUR SCHEMES HR<a name="chcolours"><h2>Colour Schemes</h2></a> ATThe RasMol AXcolour colour ATcommand allows different objects (such as atoms, bonds and ribbon segments) ATto be given a specified colour. Typically this colour is either a RasMol ATpredefined colour name or an RGB triple. Additionally RasMol also supports AXaminocolours amino, AXchaincolours chain, AXgroupcolours group, AXshapelycolours shapely, AXstructurecolours structure, AXtemperaturecolours temperature, AXusercolours user ATand AXhbondtypecolours hbond type ATcolour schemes. ATThe currently predefined colour ATnames are PTlisted below with their corresponding RGB triplet. PP PR blue [0,0,255] black [0,0,0] PR cyan [0,255,255] green [0,255,0] PR greenblue [46,139,87] magenta [255,0,255] PR orange [255,165,0] purple [160,32,240] PR red [255,0,0] redorange [255,69,0] PR violet [238,130,238] white [255,255,255] PR yellow [255,255,0] AB PR?color amino PR?colour amino ASAmino Colours ATThe RasMol ACamino ATcolour scheme colours amino acids according to traditional amino acid ATproperties. The purpose of colouring is to identify amino acids in an ATunusual or surprising environment. The outer parts of a protein are ATpolar are visible (bright) colours and non-polar residues darker. Most ATcolours are hallowed by tradition. This colour scheme is similar to the AXshapelycolours shapely ATscheme. PP PR ASP,GLU bright red [230,10,10] CYS,MET yellow [230,230,0] PR LYS,ARG blue [20,90,255] SER,THR orange [250,150,0] PR PHE,TYR mid blue [50,50,170] ASN,GLN cyan [0,220,220] PR GLY light grey [235,235,235] LEU,VAL,ILE green [15,130,15] PR ALA dark grey [200,200,200] TRP pink [180,90,180] PR HIS pale blue [130,130,210] PRO flesh [220,150,130] AB PR?chain PR?color chain PR?colour chain ASChain Colours ATThe RasMol ACchain ATcolour scheme assigns each macromolecular chain a unique colour. This ATcolour scheme is particularly usefull for distinguishing the parts of ATmultimeric structure or the individual `strands' of a DNA chain. AB PR?cpk PR?color cpk PR?colour cpk ASCPK Colours ATThe RasMol ACcpk ATcolour scheme is based upon the colours of the popular plastic ATspacefilling models which were developed by Corey, Pauling and later ATimproved by Kultun. This colour scheme colour `atom' objects by the ATatom (element) type. This is the scheme conventionally used by chemists. PTThe assignment of element type to colours is given below. PP PR Carbon light grey Chlorine green PR Oxygen red Bromine, Zinc brown PR Hydogen white Sodium blue PR Nitrogen light blue Iron purple PR Sulphur yellow Calcium, Metals dark grey PR Phosphorous orange Unknown deep pink AB PR?group PR?color group PR?colour group ASGroup Colours ATThe RasMol ACgroup ATcolour scheme colour codes residues by their position in a macromolecular ATchain. Each chain is drawn as a smooth spectrum from blue through green, ATyellow and orange to red. Hence the N terminus of proteins and 5' terminus ATof nucleic acids are coloured red and the C terminus of proteins and 3' ATterminus of nucleic acids are drawn in blue. If a chain has a large number ATof heterogenous molecules associated with it, the macromolecule may not be ATdrawn in the full `range' of the spectrum. AB PR?shapely PR?shapely colors PR?shapely colours ASShapely Colours ATThe RasMol ACshapely ATcolour scheme colour codes residues by amino acid property. This scheme ATis based upon Bob Fletterick's "Shapely Models". Each amino acid and ATnucleic acid residue is given a unique colour. The ACshapely ATcolour scheme is used by David Bacon's Raster3D program. This colour ATscheme is similar to the AXaminocolours amino ATcolour scheme. AB PR?color structure PR?colour structure ASStructure Colours ATThe RasMol ACstructure ATcolour scheme colours the molecule by protein secondary structure. ATAlpha helices are coloured magenta, PT[240,0,128], ATbeta sheets are coloured yellow, PT[255,255,0], ATturns are coloured pale blue, AT[96,128,255] ATand all other residues are coloured white. The secondary structure ATis either read from the PDB file (HELIX and SHEET records), if available, ATor determined using Kabsch and Sander's DSSP algorithm. The RasMol AXstructure structure ATcommand may be used to force DSSP's structure assignment to be used. AB PR?temperature PR?color temperature PR?colour temperature ASTemperature Colours ATThe RasMol ACtemperature ATcolour scheme colour codes each atom according to the anisotropic ATtemperature (beta) value stored in the PDB file. Typically this gives ATa measure of the mobility/uncertainty of a given atom's position. High ATvalues are coloured in warmer (red) colours and lower values in colder AT(blue) colours. This feature is often used to associate a "scale" value AT[such as amino acid variability in viral mutants] with each atom in a ATPDB file, and colour the molecule appropriately. AB PR?user PR?color user PR?colour user ASUser Colours ATThe RasMol ACuser ATcolour scheme allows RasMol to use the colour scheme stored in the ATPDB file. The colours for each atom are stored in COLO records placed ATin the PDB data file. This convention was introducted by David Bacon's ATRaster3D program. AB PR?type PR?color type PR?colour type ASHBond Type Colours ATThe RasMol ACtype ATcolour scheme applies only to hydrogen bonds, hence is used in the command AC"colour hbonds type ATThis colour scheme colour codes each hydrogen bond according to the ATdistance along a protein chain between hydrogen bond donor and acceptor. ATThis schematic representation was introduced by Belhadj-Mostefa and ATMilner-White. This representation gives a good insight into protein ATsecondary structure (hbonds forming alpha helices appear red, those ATforming sheets appear yellow and those forming turns appear magenta). PP PR Offset Colour Triple PR +2 white [255,255,255] PR +3 magenta [255,0,255] PR +4 red [255,0,0] PR +5 orange [255,165,0] PR -3 cyan [0,255,255] PR -4 green [0,255,0] PR default yellow [255,255,0] AP %% %% General Help %% PR?codes PR?amino codes PR?amino acid codes PRAmino Acid Codes PTThe following table lists the names, single letter and three letter PTcodes of each of the amino acids. PP PR Alanine A ALA Arginine R ARG PR Asparagine N ASN Aspartic acid D ASP PR Cysteine C CYS Glutamic acid E GLU PR Glutamine Q GLN Glycine G GLY PR Histidine H HIS Isoleucine I ILE PR Leucine L LEU Lysine K LYS PR Methionine M MET Phenylalanine F PHE PR Proline P PRO Serine S SER PR Threonine T THR Tryptophan W TRP PR Tyrosine Y TYR Valine V VAL PB PR?boolean PR?booleans PR?boolean expression PR?boolean expressions PRBooleans PTA boolean parameter is a truth value. Valid boolean values are `true' and PT`false', and their synonyms `on' and `off'. Boolean parameters are commonly PTused by RasMol to either enable or disable a representation or option. PP %% %% Signature %% %% MT.SH SEE ALSO MTThe RasMol User Manual! MT MT.SH AUTHOR MTCopyright (C) 1992-94 by Roger Sayle. All rights reserved. MT (rasmol@ggr.co.uk) %% %% RTF Closing %% RT}