RASMOL(1) RASMOL(1) NNAAMMEE rasmol - Molecular Graphics Visualisation Tool v2.7.1.1 SSYYNNOOPPSSIISS rraassmmooll [--nnooddiippllaayy] [[--_f_o_r_m_a_t ] _f_i_l_e_n_a_m_e] [--ssccrriipptt _s_c_r_i_p_t_f_i_l_e] FFOORRMMAATTSS --ppddbb Protein Data Bank --mmddll MDL's MOL File Format --mmooll22 Tripos' Sybyl MOL2 Format --xxyyzz MSC's XYZ (XMol) Format --mmooppaacc MOPAC Input or Output File Format --aallcchheemmyy Alchemy File Format --cchhaarrmmmm CHARMm File Format --cciiff IUCr CIF or CIF File Format NNOOTTIICCEESS This software has been created from several sources. Much of the code is from RasMol 2.6, as created by Roger Sayle. The torsion angle code, new POVRAY3 code and other fea- tures are derived from the RasMol2.6x1 revisions by Arne Mueller. The Ramachandran printer plot code was derived from fisipl created by Frances C. Bernstein. See the Protein Data Bank program tape. The CIF modifications make use of a library based in part on CBFlib by Paul J. Ellis and Herbert J. Bernstein. Parts of CBFlib is loosely based on the CIFPARSE software package from the NDB at Rutgers university. Please type the RasMol commands hheellpp ccooppyyiinngg,, hheellpp ggeenneerraall,, hheellpp IIUUCCRR,, hheellpp CCBBFFlliibb,, and hheellpp CCIIFFPPAARRSSEE for applicable notices. Please type hheellpp ccooppyyrriigghhtt for copyright notices. If you use RasMol V2.6 or an earlier version, type the RasMol command hheellpp oollddnnoottiiccee.. CCooppyyiinngg RRaassMMooll This version is based on RasMol version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4. If you are not going to make changes to RasMol, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following: 1. Either include the complete documentation, especially the file NOTICE, with what you dis- tribute or provide a clear indication where people can get a copy of the documentation; and 2. Please give credit where credit is due citing January 2001 1 RASMOL(1) RASMOL(1) the version and original authors properly; and 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind. If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following: 4. Please explain in your documentation how what you did differs from this version of RasMol; and 5. Please make your modified source code avail- able. This version of RasMol is _not_ in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol. GGeenneerraall NNoottiiccee The following notice applies to this work as a whole and to the works included within it: * Creative endeavors depend on the lively exchange of ideas. There are laws and customs which estab- lish rights and responsibilities for authors and the users of what authors create. This notice is not intended to prevent you from using the software and documents in this package, but to ensure that there are no misunderstandings about terms and con- ditions of such use. * Please read the following notice carefully. If you do not understand any portion of this notice, please seek appropriate professional legal advice before making use of the software and documents included in this software package. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is due by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors. January 2001 2 RASMOL(1) RASMOL(1) * Some of the software and documents included within this software package are the intellectual property of various parties, and placement in this package does not in any way imply that any such rights have in any way been waived or diminished. * With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. * Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its docu- mentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents and any files created by the programs are provided **AS IS** without any warranty as to cor- rectness, merchantability or fitness for any par- ticular or general use. * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCU- MENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. Subject to your acceptance of the conditions stated above, and your respect for the terms and condi- tions stated in the notices below, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the fol- lowing: 1. Either include the complete documentation, especially the file NOTICE, with what you dis- tribute or provide a clear indication where people can get a copy of the documentation; and 2. Give credit where credit is due citing the ver- sion and original authors properly; and 3. Do not give anyone the impression that the original authors are providing a warranty of any kind. In addition, you may also modify this package and create derived works provided you do the following: 4. Explain in your documentation how what you did differs from this version of RasMol; and January 2001 3 RASMOL(1) RASMOL(1) 5. Make your modified source code available. RRaassMMooll VV22..66 NNoottiiccee The following notice applies to RasMol V 2.6 and older RasMol versions. 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 pack- aging or cover other than that in which it was pro- duced. No part of this manual or accompanying soft- ware may be reproduced, stored in a retrieval sys- tem 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 pur- chaser's personal use. This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or com- munication 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, bankruptcy or outbreak of war. IIUUCCRR PPoolliiccyy TThhee IIUUCCrr PPoolliiccyy ffoorr tthhee PPrrootteeccttiioonn aanndd tthhee PPrroommoo-- ttiioonn ooff tthhee SSTTAARR FFiillee aanndd CCIIFF SSttaannddaarrddss ffoorr EExxcchhaannggiinngg aanndd AArrcchhiivviinngg EElleeccttrroonniicc DDaattaa OOvveerrvviieeww The Crystallographic Information File (CIF)[1] is a standard for information interchange promulgated by the International Union of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for submitting publications to Acta Crystal- lographica Section C and reports of crystal struc- ture determinations to other sections of Acta Crys- tallographica and many other journals. The syntax of a CIF is a subset of the more general STAR File[2] format. The CIF and STAR File approaches are used increasingly in the structural sciences for data exchange and archiving, and are having a significant influence on these activities in other fields. January 2001 4 RASMOL(1) RASMOL(1) SSttaatteemmeenntt ooff iinntteenntt The IUCr's interest in the STAR File is as a gen- eral data interchange standard for science, and its interest in the CIF, a conformant derivative of the STAR File, is as a concise data exchange and archival standard for crystallography and struc- tural science. PPrrootteeccttiioonn ooff tthhee ssttaannddaarrddss To protect the STAR File and the CIF as standards for interchanging and archiving electronic data, the IUCr, on behalf of the scientific community, * holds the copyrights on the standards them- selves, * owns the associated trademarks and service marks, and * holds a patent on the STAR File. These intellectual property rights relate solely to the interchange formats, not to the data contained therein, nor to the software used in the genera- tion, access or manipulation of the data. PPrroommoottiioonn ooff tthhee ssttaannddaarrddss The sole requirement that the IUCr, in its protec- tive role, imposes on software purporting to pro- cess STAR File or CIF data is that the following conditions be met prior to sale or distribution. * Software claiming to read files written to either the STAR File or the CIF standard must be able to extract the pertinent data from a file con- formant to the STAR File syntax, or the CIF syntax, respectively. * Software claiming to write files in either the STAR File, or the CIF, standard must produce files that are conformant to the STAR File syntax, or the CIF syntax, respectively. * Software claiming to read definitions from a specific data dictionary approved by the IUCr must be able to extract any pertinent definition which is conformant to the dictionary definition language (DDL)[3] associated with that dictionary. The IUCr, through its Committee on CIF Standards, will assist any developer to verify that software January 2001 5 RASMOL(1) RASMOL(1) meets these conformance conditions. GGlloossssaarryy ooff tteerrmmss [1] CIF: is a data file conformant to the file syn- tax defined at http://www.iucr.org/iucr- top/cif/spec/index.html [2] STAR File: is a data file conformant to the file syntax defined at http://www.iucr.org/iucr- top/cif/spec/star/index.html [3] DDL: is a language used in a data dictionary to define data items in terms of "attributes". Dictio- naries currently approved by the IUCr, and the DDL versions used to construct these dictionaries, are listed at http://www.iucr.org/iucr- top/cif/spec/ddl/index.html Last modified: 30 September 2000 IUCR Policy Copyright (C) 2000 International Union of Crystallography CCBBFFLLIIBB The following Disclaimer Notice applies to CBFlib V0.1, from which this code in part is derived. * The items furnished herewith were developed under the sponsorship of the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland Stanford Junior University, nor their employees, makes any warranty, express or implied, or assumes any lia- bility or responsibility for accuracy, completeness or usefulness of any information, apparatus, prod- uct or process disclosed, or represents that its use will not infringe privately-owned rights. Men- tion of any product, its manufacturer, or suppliers shall not, nor is it intended to, imply approval, disapproval, or fitness for any particular use. The U.S. and the University at all times retain the right to use and disseminate the furnished items for any purpose whatsoever. Notice 91 02 01 CCIIFFPPAARRSSEE Portions of this software are loosely based on the CIFPARSE software package from the NDB at Rutgers University. See http://ndbserver.rutgers.edu/NDB/mmcif/software January 2001 6 RASMOL(1) RASMOL(1) CIFPARSE is part of the NDBQUERY application, a program component of the Nucleic Acid Database Pro- ject [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.], whose cooperation is gratefully acknowledged, especially in the form of design concepts created by J. Westbrook. Please be aware of the following notice in the CIF- PARSE API: This software is provided WITHOUT WARRANTY OF MER- CHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFT- WARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. DDEESSCCRRIIPPTTIIOONN RasMol 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 wide range of architectures and operating systems includ- ing Microsoft Windows, Apple Macintosh, UNIX and VMS sys- tems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server. The program reads in a molecule coordinate file and inter- actively 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. The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Please type "help notices" for important notices. CCOOMMMMAANNDDSS RasMol allows the execution of interactive commands typed January 2001 7 RASMOL(1) RASMOL(1) at the RRaassMMooll>> prompt in the terminal window. Each command must be given on a separate line. Keywords are case insen- sitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments. The commands/keywords currently recognised by RasMol are given below. BBaacckkbboonnee The RasMol bbaacckkbboonnee command permits the representa- tion 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 parame- ter in the same way as with the wwiirreeffrraammee command. The command bbaacckkbboonnee ooffff turns off the selected 'bonds', and bbaacckkbboonnee oonn 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 ccoolloouurr bbaacckkbboonnee command. The reserved word backbone is also used as a prede- fined set ("help sets") and as a parameter to the sseett hhbboonndd and sseett ssssbboonndd commands. The RasMol com- mand ttrraaccee renders a smoothed backbone, in contrast to bbaacckkbboonnee which connects alpha carbons with straight lines. The backbone may be displayed with dashed lines by use of the bbaacckkbboonnee ddaasshh command. BBaacckkggrroouunndd The RasMol bbaacckkggrroouunndd command is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma sepa- rated triple of Red, Green and Blue (RGB) compo- nents enclosed in square brackets. Typing the com- mand hheellpp ccoolloouurrss will give a list of the prede- fined colour names recognised by RasMol. When run- ning under X Windows, RasMol also recognises colours in the X server's colour name database. The bbaacckkggrroouunndd command is synonymous with the Ras- Mol sseett bbaacckkggrroouunndd command. CCaarrttoooonn The RasMol ccaarrttoooonn command does a display of a January 2001 8 RASMOL(1) RASMOL(1) molecule rriibbbboonnss as Richardson (MolScript) style protein ccaarrttoooonnss,, implemented as thick (deep) rib- bons. The easiest way to obtain a cartoon represen- tation of a protein is to use the CCaarrttoooonnss option on the DDiissppllaayy menu. The ccaarrttoooonn command represents the currently selected residues as a deep ribbon with width specified by the command's argument. Using the command without a parameter results in the ribbon's width being taken from the protein's secondary structure, as described in the rriibbbboonnss command. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the sseett ccaarrttoooonnss command. The depth of the cartoon may be adjusted using the sseett ccaarrttoooonnss <> command. The sseett ccaarrttoooonnss command without any parameters returns these two options to their default values. CCeennttrree The RasMol cceennttrree command defines the point about which the rroottaattee command and the scroll bars rotate the current molecule. Without a parameter the cen- tre 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 sin- gle atom is specified by the expression, that atom will remain 'stationary' during rotations. Type hheellpp eexxpprreessssiioonn for more information on RasMol atom expressions. Alternatively the centring may be given as a comma separated triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the centre of gravity. The triple must be enclosed in square brackets. CClliippbbooaarrdd The RasMol cclliippbbooaarrdd command places a copy of the currently displayed image on the local graphics 'clipboard'. Note: this command is not yet sup- ported on UNIX or VMS machines. It is intended to make transfering images between applications easier under Microsoft Windows or on an Apple Macintosh. 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 wwrriittee command. January 2001 9 RASMOL(1) RASMOL(1) CCoolloouurr Colour the atoms (or other objects) of the selected region. 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 hheellpp ccoolloouurrss will give a list of all the predefined colour names recognised by Ras- Mol. Allowed objects are aattoommss,, bboonnddss,, bbaacckkbboonnee,, rriibb-- bboonnss,, llaabbeellss,, ddoottss,, hhbboonnddss and ssssbboonnddss.. If no object is specified, the default keyword aattoomm is assumed. Some colour schemes are defined for cer- tain object types. The colour scheme nnoonnee can be applied to all objects except atoms and dots, stat- ing that the selected objects have no colour of their own, but use the colour of their associated atoms (i.e. the atoms they connect). AAttoomm objects can also be coloured by aalltt,, aammiinnoo,, cchhaaiinn,, cchhaarrggee,, ccppkk,, ggrroouupp,, mmooddeell,, sshhaappeellyy,, ssttrruuccttuurree,, tteemmppeerraattuurree or uusseerr.. Hydrogen bonds can also be coloured by ttyyppee and dot surfaces can also be coloured by eelleecc-- ttrroossttaattiicc ppootteennttiiaall.. For more information type hheellpp ccoolloouurr <>.. CCoonnnneecctt The RasMol ccoonnnneecctt command is used to force RasMol to (re)calculate the connectivity of the current molecule. If the original input file contained connectivity information, this is discarded. The command ccoonnnneecctt ffaallssee uses a fast heuristic algo- rithm that is suitable for determining bonding in large bio-molecules such as proteins and nucleic acids. The command ccoonnnneecctt ttrruuee uses a slower more accurate algorithm based upon covalent radii that is more suitable to small molecules containing inorganic elements or strained rings. If no parame- ters are given, RasMol determines which algorithm to use based on the number of atoms in the input file. Greater than 255 atoms causes RasMol to use the faster implementation. This is the method used to determine bonding, if necessary, when a molecule is first read in using the llooaadd command. DDeeffiinnee The RasMol ddeeffiinnee command allows the user to asso- ciate an arbitrary set of atoms with a unique iden- tifier. This allows the definition of user-defined sets. These sets are declared statically, i.e. once defined the contents of the set do not change, even if the expression defining them depends on the cur- rent transformation and representation of the molecule. January 2001 10 RASMOL(1) RASMOL(1) DDoottss The RasMol ddoottss command is used to generate a van der Waals' dot surface around the currently selected atoms. Dot surfaces display regularly spaced points on a sphere of van der Waals' radius about each selected atom. Dots that would are 'buried' within the van der Waals' radius of any other atom (selected or not) are not displayed. The command ddoottss oonn deletes any existing dot sur- face and generates a dots surface around the cur- rently selected atom set with a default dot density of 100. The command ddoottss ooffff deletes any existing dot surface. The dot density may be specified by providing a numeric parameter between 1 and 1000. This value approximately corresponds to the number of dots on the surface of a medium sized atom. By default, the colour of each point on a dot sur- face is the colour of its closest atom at the time the surface is generated. The colour of the whole dot surface may be changed using the ccoolloouurr ddoottss command. EEcchhoo The RasMol eecchhoo command is used to display a mes- sage in the RasMol command/terminal window. The string parameter may optionally be delimited in double quote characters. If no parameter is speci- fied, the eecchhoo command displays a blank line. This command is particularly useful for displaying text from within a RasMol ssccrriipptt file. EEnngglliisshh The RasMol EEnngglliisshh command sets the menus and mes- sages to the English versions. The command SSppaanniisshh may be used to select Spanish menus and messages. HHBBoonnddss The RasMol hhbboonndd command is used to represent the hydrogen bonding of the protein molecule's back- bone. This information is useful in assessing the protein's secondary structure. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The first time the hhbboonndd command is used, the program searches the structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The command hhbboonnddss oonn displays the selected 'bonds' as dotted lines, and the hhbboonnddss ooffff turns off their display. The colour of hbond objects may be changed by the ccoolloouurr hhbboonndd command. Initially, each hydrogen bond has the colours of its connected atoms. January 2001 11 RASMOL(1) RASMOL(1) By default the dotted lines are drawn between the accepting oxygen and the donating nitrogen. By using the sseett hhbboonnddss command the alpha carbon posi- tions of the appropriate residues may be used instead. This is especially useful when examining proteins in backbone representation. HHeellpp The RasMol hheellpp command provides on-line help on the given topic. LLaabbeell The RasMol llaabbeell command allows an arbitrary for- matted text string to be associated with each cur- rently selected atom. This string may contain embedded 'expansion specifiers' which display prop- erties of the atom being labelled. An expansion specifier consists of a '%' character followed by a single alphabetic character specifying the property to be displayed. An actual '%' character may be displayed by using the expansion specifier '%%'. Atom labelling for the currently selected atoms may be turned off with the command llaabbeell ooffff.. By default, if no string is given as a parameter, Ras- Mol uses labels appropriate for the current molecule. The colour of each label may be changed using the ccoolloouurr llaabbeell command. By default, each label is drawn in the same colour as the atom to which it is attached. The size and spacing of the displayed text may be changed using the sseett ffoonnttssiizzee command. The width of the strokes in the displayed text may be changed using the sseett ffoonnttssttrrookkee command. LLooaadd Load a molecule coordinate file into RasMol. Valid molecule file formats are ppddbb (Protein Data Bank format), mmddll (Molecular Design Limited's MOL file format), aallcchheemmyy (Tripos' Alchemy file format), mmooll22 (Tripos' Sybyl Mol2 file format), cchhaarrmmmm (CHARMm file format), xxyyzz (MSC's XMol XYZ file for- mat), mmooppaacc (J. P. Stewart's MOPAC file format) or cciiff (IUCr CIF or mmCIF file format). If no file format is specified, PPDDBB,, CCIIFF,, or mmmmCCIIFF is assumed by default. Only a single molecule may be loaded at a time. To delete a molecule prior to loading another use the RasMol zzaapp command. The llooaadd command selects all the atoms in the molecule, centres it on the screen and renders it January 2001 12 RASMOL(1) RASMOL(1) as a CPK coloured wireframe model. If the molecule contains no bonds (i.e. contains only alpha car- bons), it is drawn as an alpha carbon backbone. If the file specifies fewer bonds than atoms, RasMol determines connectivity using the ccoonnnneecctt command. The llooaadd iinnlliinnee command also allows the storing of atom coordinates in scripts to allow better inte- gration with WWW browsers. A load command executed inside a script file may specify the keyword iinnlliinnee instead of a conventional filename. This option specifies that the coordinates of the molecule to load are stored in the same file as the currently executing commands. MMoonniittoorr The RasMol mmoonniittoorr command allows the display of distance monitors. A distance monitor is a dashed (dotted) line between an arbitrary pair of atoms, optionally labelled by the distance between them. The RasMol command mmoonniittoorr <> <> adds such a distance monitor between the two atoms spec- ified by the atom serial numbers given as parame- ters Distance monitors are turned off with the command mmoonniittoorrss ooffff.. By default, monitors display the distance between its two end points as a label at the centre of the monitor. These distance labels may be turned off with the command sseett mmoonniittoorrss ooffff,, and re-enabled with the command sseett mmoonniittoorrss oonn.. Like most other representations, the colour of a monitor is taken from the colour of its end points unless specified by the ccoolloouurr mmoonniittoorrss com- mand. Distance monitors may also be added to a molecule interactively with the mouse, using the sseett ppiicckkiinngg mmoonniittoorr command. Clicking on an atom results in its being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that, in monitor mode, every second atom displays the distance between this atom and the previous one. The shift key may be used to form distance monitors between a fixed atom and several consecutive positions. A distance monitor may also be removed (toggled) by selecting the appropriate pair of atom end points a second time. PPaauussee The RasMol ppaauussee command is used in script files to stop the script file for local manipulation by a mouse, until any key is pushed to restart the January 2001 13 RASMOL(1) RASMOL(1) script file. WWaaiitt is synonymous with ppaauussee.. This command may be executed in RasMol script files to suspend the sequential execution of commands and allow the user to examine the current image. When RasMol executes a ppaauussee command in a script file, it suspends execution of the rest of the file, refreshes the image on the screen and allows the manipulation of the image using the mouse and scroll bars, or resizing of the graphics window. Once a key is pressed, control returns to the script file at the line following the ppaauussee com- mand. While a script is suspended the molecule may be rotated, translated, scaled, slabbed and picked as usual, but all menu commands are disabled. PPrriinntt The RasMol pprriinntt command sends the currently dis- played image to the local default printer using the operating system's native printer driver. Note: this command is not yet supported under UNIX or VMS. It is intended to take advantage of Microsoft Windows and Apple Macintosh printer drivers. For example, this allows images to be printed directly on a dot matrix printer. When using RasMol on a UNIX or VMS system this functionality may be achieved by either generating a PostScript file using the RasMol wwrriittee ppss or wwrriittee vveeccttppss commands and printing that or generat- ing a raster image file and using a utility to dump that to the local printer. QQuuiitt Exit from the RasMol program. The RasMol commands eexxiitt and qquuiitt are synonymous, except within nested scripts. In that case, eexxiitt terminates only the current level, while qquuiitt terminates all nested levels of scripts. RReeffrreesshh The RasMol rreeffrreesshh command redraws the current image. This is useful in scripts to ensure appli- cation of a complex list of parameter changes. RReennuummbbeerr The RasMol rreennuummbbeerr command sequentially numbers the residues in a macromolecular chain. The optional parameter specifies the value of the first residue in the sequence. By default, this value is one. For proteins, each amino acid is numbered con- secutively from the N terminus to the C terminus. For nucleic acids, each base is numbered from the January 2001 14 RASMOL(1) RASMOL(1) 5' terminus to the 3' terminus. All chains in the current database are renumbered and gaps in the original sequence are ignored. The starting value for numbering may be negative. RReesseett The RasMol rreesseett command restores the original viewing transformation and centre of rotation. The scale is set to its default value, zzoooomm 110000,, the centre of rotation is set to the geometric centre of the currently loaded molecule, cceennttrree aallll,, this centre is translated to the middle of the screen and the viewpoint set to the default orientation. This command should not be mistaken for the RasMol zzaapp command which deletes the currently stored molecule, returning the program to its initial state. RReessttrriicctt The RasMol rreessttrriicctt command both defines the cur- rently selected region of the molecule and disables the representation of (most of) those parts of the molecule no longer selected. All subsequent RasMol commands that modify a molecule's colour or repre- sentation affect only the currently selected region. The parameter of a rreessttrriicctt command is a RasMol atom expression that is evaluated for every atom of the current molecule. This command is very similar to the RasMol sseelleecctt command, except rreessttrriicctt disables the wwiirreeffrraammee,, ssppaacceeffiillll and bbaacckkbboonnee representations in the non-selected region. Type "help expression" for more information on Ras- Mol atom expressions. RRiibbbboonnss The RasMol rriibbbboonnss command displays the currently loaded protein or nucleic acid as a smooth solid "ribbon" surface passing along the backbone of the protein. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The colour of the ribbon is changed by the RasMol ccoolloouurr rriibbbboonn command. If the current ribbon colour is nnoonnee (the default), the colour is taken from the alpha carbon at each position along its length. The width of the ribbon at each position is deter- mined by the optional parameter in the usual RasMol units. By default the width of the ribbon is taken from the secondary structure of the protein or a January 2001 15 RASMOL(1) RASMOL(1) constant value of 720 (2.88 Angstroms) for nucleic acids. The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The sec- ondary structure assignment is either from the PDB file or calculated using the DSSP algorithm as used by the ssttrruuccttuurree command. This command is similar to the RasMol command ssttrraannddss which renders the biomolecular ribbon as parallel depth-cued curves. RRoottaattee Rotate the molecule about the specified axis. Per- mitted values for the axis parameter are "x", "y" and "z". The integer parameter states the angle in degrees for the structure to be rotated. For the X and Y axes, positive values move the closest point up and right, and negative values move it down and left, respectively. For the Z axis, a positive rotation acts clockwise and a negative angle anti- clockwise. SSaavvee Save the currently selected set of atoms in a Pro- tein Data Bank (PDB), MDL, Alchemy(tm) or XYZ for- mat file. The distinction between this command and the RasMol wwrriittee command has been dropped. The only difference is that without a format specifier the ssaavvee command generates a PPDDBB file and the wwrriittee command generates a GGIIFF image. SSccrriipptt The RasMol ssccrriipptt command reads a set of RasMol commands sequentially from a text file and executes them. This allows sequences of commonly used com- mands to be stored and performed by single command. A RasMol script file may contain a further script command up to a maximum "depth" of 10, allowing complicated sequences of actions to be executed. RasMol ignores all characters after the first '#' character on each line allowing the scripts to be annotated. Script files are often also annotated using the RasMol eecchhoo command. The most common way to generate a RasMol script file is to use the wwrriittee ssccrriipptt or wwrriittee rraassmmooll commands to output the sequence of commands that are needed to regenerate the current view, repre- sentation and colouring of the currently displayed molecule. The RasMol command ssoouurrccee is synonymous with the ssccrriipptt command. January 2001 16 RASMOL(1) RASMOL(1) SSeelleecctt Define the currently selected region of the molecule. All subsequent RasMol commands that manipulate a molecule or modify its colour or rep- resentation only affect the currently selected region. The parameter of a sseelleecctt command is a Ras- Mol expression that is evaluated for every atom of the current molecule. The currently selected (active) region of the molecule are those atoms that cause the expression to evaluate true. To select the whole molecule use the RasMol command sseelleecctt aallll.. The behaviour of the sseelleecctt command without any parameters is determined by the RasMol hheetteerroo and hhyyddrrooggeenn parameters. Type "help expression" for more information on Ras- Mol atom expressions. SSeett The RasMol sseett command allows the user to alter various internal program parameters such as those controlling rendering options. Each parameter has its own set or permissible parameter options. Typi- cally, omitting the paramter option resets that parameter to its default value. A list of valid parameter names is given below. SShhooww The RasMol sshhooww command display details of the sta- tus of the currently loaded molecule. The command sshhooww iinnffoorrmmaattiioonn lists the molecule's name, classi- fication, PDB code and the number of atoms, chains, groups it contains. If hydrogen bonding, disul- phide bridges or secondary structure have been determined, the number of hbonds, ssbonds, helices, ladders and turns are also displayed, respectively. The command sshhooww pphhiippssii shows the phi and psi angles of the currently selected residues and the omega angles of cis peptide bonds. The command sshhooww RRaammPPrriinntt (or 'show RPP' or 'show RamachandranPrint- erPlot') shows a simple Ramachandran printer plot in the style of Frances Bernstein's fisipl program. The command sshhooww sseelleecctteedd (or 'show selected group' or 'show selected chain' or 'show selected atom' ) shows the groups (default), chains or atoms of the current selection. The command sshhooww sseeqquueennccee lists the residues that comprise each chain of the molecule. The command sshhooww ssyymmmmeettrryy shows the space group and unit cell of the molecule. SSllaabb The RasMol ssllaabb command enables, disables or posi- tions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing January 2001 17 RASMOL(1) RASMOL(1) plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values deter- mine the percentage of the molecule to be drawn. SSppaacceeffiillll The RasMol ssppaacceeffiillll command is used to represent all of the currently selected atoms as solid spheres. This command is used to produce both union-of-spheres and ball-and-stick models of a molecule. The command, ssppaacceeffiillll ttrruuee,, the default, represents each atom as a sphere of van der Waals radius. The command ssppaacceeffiillll ooffff turns off the representation of the selected atom as spheres. A sphere radius may be specified as an integer in RasMol units (1/250th Angstrom) or a value contain- ing a decimal point. A value of 500 (2.0 Angstroms) or greater results in a "Parameter value too large" error. The tteemmppeerraattuurree option sets the radius of each sphere to the value stored in its temperature field. Zero or negative values have no effect and values greater than 2.0 are truncated to 2.0. The uusseerr option allows the radius of each sphere to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOUR record extension. The RasMol command ccppkk is synonymous with the ssppaacceeffiillll command. SSppaanniisshh The RasMol SSppaanniisshh command sets the menus and mes- sages to the Spanish versions. The command EEnngglliisshh may be used to select English menus and messages. SSSSBBoonnddss The RasMol ssssbboonnddss command is used to represent the disulphide bridges of the protein molecule as either dotted lines or cylinders between the con- nected cysteines. The first time that the ssssbboonnddss command is used, the program searches the structure of the protein to find half-cysteine pairs (cys- teines whose sulphurs are within 3 Angstroms of each other) and reports the number of bridges to the user. The command ssssbboonnddss oonn displays the selected "bonds" as dotted lines, and the command ssssbboonnddss ooffff disables the display of ssbonds in the currently selected area. Selection of disulphide bridges is identical to normal bonds, and may be adjusted using the RasMol sseett bboonnddmmooddee command. The January 2001 18 RASMOL(1) RASMOL(1) colour of disulphide bonds may be changed using the ccoolloouurr ssssbboonnddss command. By default, each disulphide bond has the colours of its connected atoms. By default disulphide bonds are drawn between the sulphur atoms within the cysteine groups. By using the sseett ssssbboonnddss command the position of the cys- teine's alpha carbons may be used instead. SSttaarr The RasMol ssttaarr command is used to represent all of the currently selected atoms as stars (six strokes, one each in the x, -x, y, -y, z and -z directions). The commands sseelleecctt nnoott bboonnddeedd followed by ssttaarr 7755 are useful to mark unbonded atoms in a wwiirreeffrraammee display with less overhead than provided by ssppaaccee-- ffiillll 7755.. This can be done automatically for all subsequent wireframe displays with the command sseett bboonnddmmooddee nnoott bboonnddeedd.. The command ssttaarr ttrruuee,, the default, represents each atom as a star with strokes length equal to van der Waals radius. The command ssttaarr ooffff turns off the representation of the selected atom as stars. A star stroke length may be specified as an integer in RasMol units (1/250th Angstrom) or a value con- taining a decimal point. A value of 500 (2.0 Angstroms) or greater results in a "Parameter value too large" error. The tteemmppeerraattuurree option sets the stroke length of each star to the value stored in its temperature field. Zero or negative values have no effect and values greater than 2.0 are truncated to 2.0. The uusseerr option allows the stroke length of each star to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOUR record extension. The RasMol ssppaacceeffiillll command can be used for more artistic rendering of atoms as spheres. SStteerreeoo The RasMol sstteerreeoo command provides side-by-side stereo display of images. Stereo viewing of a molecule may be turned on (and off) either by selecting SStteerreeoo from the OOppttiioonnss menu, or by typ- ing the commands sstteerreeoo oonn or sstteerreeoo ooffff.. The sep- aration angle between the two views may be adjusted with the sseett sstteerreeoo [[--]] <> command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. The inclusion of [[--]] <> in the sstteerreeoo com- mand, as for example in sstteerreeoo 33 or sstteerreeoo --55,, also January 2001 19 RASMOL(1) RASMOL(1) controls angle and direction. The stereo command is only partially implemented. When stereo is turned on, the image is not properly recentred. (This can be done with a ttrraannssllaattee xx --<> command.) It is not supported in vector PostScript output files, is not saved by the wwrriittee ssccrriipptt command, and in general is not yet properly interfaced with several other features of the pro- gram. SSttrraannddss The RasMol ssttrraannddss command displays the currently loaded protein or nucleic acid as a smooth "ribbon" of depth-cued curves passing along the backbone of the protein. The ribbon is composed of a number of strands that run parallel to one another along the peptide plane of each residue. The ribbon is drawn between each amino acid whose alpha carbon is cur- rently selected. The colour of the ribbon is changed by the RasMol ccoolloouurr rriibbbboonn command. If the current ribbon colour is nnoonnee (the default), the colour is taken from the alpha carbon at each posi- tion along its length. The central and outermost strands may be coloured independently using the ccoolloouurr rriibbbboonn11 and ccoolloouurr rriibbbboonn22 commands, respec- tively. The number of strands in the ribbon may be altered using the RasMol sseett ssttrraannddss command. The width of the ribbon at each position is deter- mined by the optional parameter in the usual RasMol units. By default the width of the ribbon is taken from the secondary structure of the protein or a constant value of 720 for nucleic acids (which pro- duces a ribbon 2.88 Angstroms wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The secondary structure assignment is either from the PDB file or calcu- lated using the DSSP algorithm as used by the ssttrruuccttuurree command. This command is similar to the RasMol command rriibbbboonnss which renders the biomolecu- lar ribbon as a smooth shaded surface. SSttrruuccttuurree The RasMol ssttrruuccttuurree command calculates secondary structure assignments for the currently loaded pro- tein. If the original PDB file contained structural assignment records (HELIX, SHEET and TURN) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been January 2001 20 RASMOL(1) RASMOL(1) done already. The secondary structure is then determined using Kabsch and Sander's DSSP algo- rithm. Once finished the program reports the number of helices, strands and turns found. TTrraaccee The RasMol ttrraaccee command displays a smooth spline between consecutive alpha carbon positions. This spline does not pass exactly through the alpha car- bon position of each residue, but follows the same path as rriibbbboonnss,, ssttrraannddss and ccaarrttoooonnss.. Note that residues may be displayed as rriibbbboonnss,, ssttrraannddss,, ccaarr-- ttoooonnss or as a ttrraaccee.. Enabling one of these repre- sentations disables the others. However, a residue may be displayed simultaneously as backbone and as one of the above representations. This may change in future versions of RasMol. Prior to version 2.6, ttrraaccee was synonymous with bbaacckkbboonnee.. TTrraaccee tteemmppeerraattuurree displays the backbone as a wider cylinder at high temperature factors and thinner at lower. This representation is useful to X-ray crystallographers and NMR spectroscopists. TTrraannssllaattee The RasMol ttrraannssllaattee command moves the position of the centre of the molecule on the screen. The axis parameter specifies along which axis the molecule is to be moved and the integer parameter specifies the absolute position of the molecule centre from the middle of the screen. Permitted values for the axis parameter are "x", "y" and "z". Displacement values must be between -100 and 100 which corre- spond to moving the current molecule just off the screen. A positive "x" displacement moves the molecule to the right, and a positive "y" displace- ment moves the molecule down the screen. The pair of commands ttrraannssllaattee xx 00 and ttrraannssllaattee yy 00 centres the molecule on the screen. WWiirreeffrraammee The RasMol wwiirreeffrraammee command represents each bond within the selected region of the molecule as a cylinder, a line or a depth-cued vector. The dis- play of bonds as depth-cued vectors (drawn darker the further away from the viewer) is turned on by the command wwiirreeffrraammee or wwiirreeffrraammee oonn.. The selected bonds are displayed as cylinders by speci- fying a radius either as an integer in RasMol units or containing a decimal point as a value in Angstroms. A parameter value of 500 (2.0 Angstroms) or above results in an "Parameter value January 2001 21 RASMOL(1) RASMOL(1) too large" error. Bonds may be coloured using the ccoolloouurr bboonnddss command. Non-bonded atoms, which could become invisible in an ordinary wwiirreeffrraammee display can be marked by a preceding sseett bboonnddmmooddee nnoott bboonnddeedd command. If nearly co-linear bonds to atoms cause them to be difficult to see in a wireframe display, the sseett bboonnddmmooddee aallll command will add markers for aallll atoms in subsequent wwiirreeffrraammee command executions. WWrriittee Write the current image to a file in a standard format. Currently supported image file formats include bbmmpp (Microsoft bitmap) and ggiiff (Compuserve GIF), iirriiss (IRIS RGB), ppppmm (Portable Pixmap), rraass (Sun rasterfile), ppss and eeppssff (Encapsulated PostScript), mmoonnooppss (Monochrome Encapsulated PostScript), ppiicctt (Apple PICT), vveeccttppss (Vector Postscript). The wwrriittee command may also be used to generate command scripts for other graphics pro- grams. The format ssccrriipptt writes out a file contain- ing the RasMol ssccrriipptt commands to reproduce the current image. The format mmoollssccrriipptt writes out the commands required to render the current view of the molecule as ribbons in Per Kraulis' Molscript pro- gram and the format kkiinneemmaaggee the commands for David Richardson's program Mage. The following formats are useful for further processing: ppoovvrraayy (POVRay 2), ppoovvrraayy33 (POVRay 3 -- under development), vvrrmmll (VRML file). Finally, several formats are provided to provide phi-psi data for listing or for pphhiippssii (phi-psi data as an annotated list with cis omegas), rraammaacchhaann and RRDDFF and RRaammaacchhaannddrraannDDaattaaFFiillee (phi-psi data as columns of numbers for gnuplot), RRPPPP and RRaammaacchhaannddrraannPPrriinntteerrPPlloott (phi-psi data as a printer plot). The distinction between this command and the RasMol ssaavvee command has been dropped. The only difference is that without a format specifier the ssaavvee command generates a PPDDBB file and the wwrriittee command gener- ates a GGIIFF image. ZZaapp Deletes the contents of the current database and resets parameter variables to their initial default state. ZZoooomm Change the magnification of the currently displayed image. Boolean parameters either magnify or reset the scale of current molecule. An integer parameter specifies the desired magnification as a percentage January 2001 22 RASMOL(1) RASMOL(1) of the default scale. The minimum parameter value is 10; the maximum parameter value is dependent upon the size of the molecule being displayed. For medium sized proteins this is about 500. SSEETT PPAARRAAMMEETTEERRSS RasMol has a number of internal parameters that may be modified using the sseett command. These parameters control a number of program options such as rendering options and mouse button mappings. SSeett AAmmbbiieenntt The RasMol aammbbiieenntt parameter is used to control the amount of ambient (or surrounding) light in the scene. The aammbbiieenntt value must be between 0 and 100. It controls the percentage intensity of the darkest shade of an object. For a solid object, this is the intensity of surfaces facing away from the light source or in shadow. For depth-cued objects this is the intensity of objects furthest from the viewer. This parameter is commonly used to correct for mon- itors with different "gamma values" (brightness), to change how light or dark a hardcopy image appears when printed or to alter the feeling of depth for wireframe or ribbon representations. SSeett AAxxeess The RasMol aaxxeess parameter controls the display of orthogonal coordinate axes on the current display. The coordinate axes are those used in the molecule data file, and the origin is the centre of the molecule's bounding box. The sseett aaxxeess command is similar to the commands sseett bboouunnddbbooxx and sseett uunniitt-- cceellll that display the bounding box and the crystal- lographic unit cell, respectively. SSeett BBaacckkffaaddee The RasMol bbaacckkffaaddee parameter is used to control backfade to the specified background colour, rather than black. This is controlled by the commands sseett bbaacckkffaaddee oonn and sseett bbaacckkffaaddee ooffff.. For example, this may be used to generate depth-cued images that fade to white, rather than black. SSeett BBaacckkggrroouunndd The RasMol bbaacckkggrroouunndd parameter is used to set the colour of the "canvas" background. The colour may January 2001 23 RASMOL(1) RASMOL(1) be given as either a colour name or a comma sepa- rated triple of Red, Green, Blue (RGB) components enclosed in square brackets. Typing the command hheellpp ccoolloouurrss 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. The command sseett bbaacckkggrroouunndd is synonymous with the RasMol command bbaacckkggrroouunndd.. SSeett BBoonnddMMooddee The RasMol sseett bboonnddmmooddee command controls the mecha- nism used to select individual bonds and modifies the display of bonded and non-bonded atoms by sub- sequent wwiirreeffrraammee commands. When using the sseelleecctt and rreessttrriicctt commands, a given bond will be selected if i) the bondmode is oorr and either of the connected atoms is selected, or ii) the bondmode is aanndd and both atoms connected by the bond are selected. Hence an individual bond may be uniquely identified by using the command sseett bboonnddmmooddee aanndd and then uniquely selecting the atoms at both ends. The bboonnddmmooddee [[aallll || nnoonnee || nnoott bboonnddeedd]] commands add ssttaarr 7755 or ssppaacceeffiillll 7755 markers for the designated atoms to wwiirreeffrraammee displays. Stars are used when the specified wireframe radius is zero. SSeett BBoonnddss The RasMol bboonnddss parameter is used to control dis- play of double and triple bonds as multiple lines or cylinders. Currently bond orders are only read from MDL Mol files, Sybyl Mol2 format files, Tri- pos Alchemy format files, CIF and mmCIF, and suit- able PDB files. Double (and triple) bonds are specified in some PDB files by specifying a given bond twice (and three times) in CONECT records. The command sseett bboonnddss oonn enables the display of bond orders, and the command sseett bboonnddss ooffff dis- ables them. SSeett BBoouunnddBBooxx The RasMol bboouunnddbbooxx parameter controls the display of the current molecule's bounding box on the dis- play. The bounding box is orthogonal to the data file's original coordinate axes. The sseett bboouunnddbbooxx command is similar to the commands sseett aaxxeess and sseett uunniittcceellll that display orthogonal coordinate axes January 2001 24 RASMOL(1) RASMOL(1) and the bounding box, respectively. SSeett CCaarrttoooonn The RasMol ccaarrttoooonn parameter is used to control display of the cartoon version of the rriibbbboonnss dis- play. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the sseett ccaarrttoooonnss <> command. The depth of the cartoon may be adjusted using the ccaarrttoooonnss <> command. The sseett ccaarrttoooonnss command without any parameters returns these two options to their default values. SSeett CCiissAAnnggllee The RasMol cciissaannggllee parameter controls the cutoff angle for identifying cis peptide bonds. If no value is given, the cutoff is set to 90 degrees. SSeett DDiissppllaayy This command controls the display mode within Ras- Mol. By default, sseett ddiissppllaayy nnoorrmmaall,, RasMol dis- plays the molecule in the representation specified by the user. The command sseett ddiissppllaayy sseelleecctteedd changes the display mode such that the molecule is temporarily drawn so as to indicate currently selected portion of the molecule. The user speci- fied colour scheme and representation remains unchanged. In this representation all selected atoms are shown in yellow and all non selected atoms are shown in blue. The colour of the back- ground is also changed to a dark grey to indicate the change of display mode. This command is typi- cally only used by external Graphical User Inter- faces (GUIs). SSeett FFoonnttSSiizzee The RasMol sseett ffoonnttssiizzee command is used to control the size of the characters that form atom labels. This value corresponds to the height of the dis- played character in pixels. The maximum value of ffoonnttssiizzee is 48 pixels, and the default value is 8 pixels high. Fixed or proportional spacing may be selected by appending the "FS" or "PS" modifiers, respectively. The default is "FS". To display atom labels on the screen use the RasMol llaabbeell com- mand and to change the colour of displayed labels, use the ccoolloouurr llaabbeellss command. January 2001 25 RASMOL(1) RASMOL(1) SSeett FFoonnttSSttrrookkee The RasMol sseett ffoonnttssttrrookkee command is used to con- trol the size of the stroke width of the characters that form atom labels. This value is the radius in pixels of cylinders used to form the strokes. The special value of "0" is the default used for the normal single pixel stroke width, which allows for rapid drawing and rotation of the image. Non-zero values are provided to allow for more artistic atom labels for publication at the expense of extra time in rendering the image. When wider strokes are used, a larger font size is recommend, e.g. by using the RasMol sseett ffoonnttssiizzee 2244 PPSS command, followed by sseett ffoonnttssttrrookkee 22 To display atom labels on the screen use the RasMol llaabbeell command, and to change the colour of dis- played labels use the ccoolloouurr llaabbeellss command. SSeett HHBBoonnddss The RasMol hhbboonnddss parameter determines whether hydrogen bonds are drawn between the donor and acceptor atoms of the hydrogen bond, sseett hhbboonnddss ssiiddeecchhaaiinn or between the alpha carbon atoms of the protein backbone and between the phosphorous atoms of the nucleic acid backbone, sseett hhbboonnddss bbaacckkbboonnee.. The actual display of hydrogen bonds is controlled by the hhbboonnddss command. Drawing hydrogen bonds between protein alpha carbons or nucleic acid phos- phorous atoms is useful when the rest of the molecule is shown in only a schematic representa- tion such as bbaacckkbboonnee,, rriibbbboonnss or ssttrraannddss.. This parameter is similar to the RasMol ssssbboonnddss parame- ter. SSeett HHeetteerroo The RasMol hheetteerroo parameter is used to modify the 'default' behaviour of the RasMol sseelleecctt command, i.e. the behaviour of sseelleecctt without any parame- ters. When this value is ffaallssee,, the default sseelleecctt region does not include any heterogeneous atoms (refer to the predefined set hheetteerroo ). When this value is ttrruuee,, the default sseelleecctt region may con- tain hetero atoms. This parameter is similar to the RasMol hhyyddrrooggeenn parameter which determines whether hydrogen atoms should be included in the default set. If both hheetteerroo and hhyyddrrooggeenn are ttrruuee,, sseelleecctt without any parameters is equivalent to sseelleecctt aallll.. January 2001 26 RASMOL(1) RASMOL(1) SSeett HHoouurrGGllaassss The RasMol hhoouurrggllaassss parameter allows the user to enable and disable the use of the 'hour glass' cur- sor used by RasMol to indicate that the program is currently busy drawing the next frame. The command sseett hhoouurrggllaassss oonn enables the indicator, whilst sseett hhoouurrggllaassss ooffff prevents RasMol from changing the cursor. This is useful when spinning the molecule, running a sequence of commands from a script file or using interprocess communication to execute com- plex sequences of commands. In these cases a 'flashing' cursor may be distracting. SSeett HHyyddrrooggeenn The RasMol hhyyddrrooggeenn parameter is used to modify the "default" behaviour of the RasMol sseelleecctt command, i.e. the behaviour of sseelleecctt without any parame- ters. When this value is ffaallssee,, the default sseelleecctt region does not include any hydrogen, deuterium or tritium atoms (refer to the predefined set hhyyddrrooggeenn ). When this value is ttrruuee,, the default sseelleecctt region may contain hydrogen atoms. This parameter is similar to the RasMol hheetteerroo parameter which determines whether heterogeneous atoms should be included in the default set. If both hhyyddrrooggeenn and hheetteerroo are ttrruuee,, sseelleecctt without any parameters is equivalent to sseelleecctt aallll.. SSeett KKiinneemmaaggee The RasMol sseett kkiinneemmaaggee command controls the amount of detail stored in a Kinemage output file gener- ated by the RasMol wwrriittee kkiinneemmaaggee command. The out- put kinemage files are intended to be displayed by David Richardson's Mage program. sseett kkiinneemmaaggee ffaallssee,, the default, only stores the currently dis- played representation in the generated output file. The command sseett kkiinneemmaaggee ttrruuee,, generates a more complex Kinemage that contains both the wireframe and backbone representations as well as the coordi- nate axes, bounding box and crystal unit cell. SSeett MMeennuuss The RasMol sseett mmeennuuss command enables the canvas window's menu buttons or menu bar. This command is typically only used by graphical user interfaces or to create as large an image as possible when using Microsoft Windows. SSeett MMoonniittoorr The RasMol sseett mmoonniittoorr command enables mmoonniittoorrss.. January 2001 27 RASMOL(1) RASMOL(1) The distance monitor labels may be turned off with the command sseett mmoonniittoorr ooffff,, and re-enabled with the command sseett mmoonniittoorr oonn.. SSeett MMoouussee The RasMol sseett mmoouussee command sets the rotation, translation, scaling and zooming mouse bindings. The default value is rraassmmooll which is suitable for two button mice (for three button mice the second and third buttons are synonymous); X-Y rotation is controlled by the first button, and X-Y translation by the second. Additional functions are controlled by holding a modifier key on the keyboard. [Shift] and the first button performs scaling, [shift] and the second button performs Z-rotation, and [con- trol] and the first mouse button controls the clip- ping plane. The iinnssiigghhtt and qquuaannttaa options provide the same mouse bindings as other packages for expe- rienced users. SSeett PPiicckkiinngg The RasMol sseett ppiicckkiinngg series of commands affects how a user may interact with a molecule displayed on the screen in RasMol. EEnnaabblliinngg//DDiissaabblliinngg AAttoomm PPiicckkiinngg:: Clicking on an atom with the mouse results in identification and the display of its residue name, residue number, atom name, atom serial number and chain in the com- mand window. This behavior may be disabled with the command sseett ppiicckkiinngg nnoonnee and restored with the com- mand sseett ppiicckkiinngg iiddeenntt.. The command sseett ppiicckkiinngg ccoooorrdd adds the atomic coordinates of the atom to the display. Disabling picking, by using sseett ppiicckkiinngg ooffff is use- ful when executing the ppaauussee command in RasMol scripts as it prevents the display of spurious mes- sage on the command line while the script is sus- pended. MMeeaassuurriinngg DDiissttaanncceess,, AAnngglleess aanndd TToorrssiioonnss:: Interac- tive measurement of distances, angles and torsions is achieved using the commands: sseett ppiicckkiinngg ddiiss-- ttaannccee,, sseett ppiicckkiinngg mmoonniittoorr,, sseett ppiicckkiinngg aannggllee and sseett ppiicckkiinngg ttoorrssiioonn,, respectively. In these modes, clicking on an atom results in it being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that in distance mode, every second atom displays the dis- tance (or distance monitor) between this atom and January 2001 28 RASMOL(1) RASMOL(1) the previous one. In angle mode, every third atom displays the angle between the previous three atoms and in torsion mode every fourth atom displays the torsion between the last four atoms. By holding down the shift key while picking an atom, this mod- ulo counter is not incremented and allows, for example, the distances of consecutive atoms from a fixed atom to be displayed. See the mmoonniittoorr command for how to control the display of distance monitor lines and labels. LLaabbeelllliinngg AAttoommss wwiitthh tthhee MMoouussee:: The mouse may also be used to toggle the display of an atom label on a given atom. The RasMol command sseett ppiicckkiinngg llaabbeell removes a label from a picked atom if it already has one or displays a concise label at that atom position otherwise. CCeennttrriinngg RRoottaattiioonn wwiitthh tthhee MMoouussee:: A molecule may be centred on a specified atom position using the Ras- Mol commands sseett ppiicckkiinngg cceennttrree or sseett ppiicckkiinngg cceenn-- tteerr.. In this mode, picking an atom causes all futher rotations to be about that point. SSeett RRaaddiiuuss The RasMol sseett rraaddiiuuss command is used to alter the behaviour of the RasMol ddoottss command depending upon the value of the ssoollvveenntt parameter. When ssoollvveenntt is ttrruuee,, the rraaddiiuuss parameter controls whether a true van der Waals' surface is generated by the ddoottss command. If the value of rraaddiiuuss is anything other than zero, that value is used as the radius of each atom instead of its true vdW value. When the value of ssoollvveenntt is ttrruuee,, this parameter deter- mines the 'probe sphere' (solvent) radius. The parameter may be given as an integer in rasmol units or containing a decimal point in Angstroms. The default value of this parameter is determined by the value of ssoollvveenntt and changing ssoollvveenntt resets rraaddiiuuss to its new default value. SSeett SShhaaddooww The RasMol sseett sshhaaddooww command enables and disables ray-tracing of the currently rendered image. Cur- rently only the spacefilling representation is shadowed or can cast shadows. Enabling shadowing will automatically disable the Z-clipping (slab- bing) plane using the command ssllaabb ooffff.. Ray-trac- ing typically takes about several seconds for a moderately sized protein. It is recommended that shadowing be normally disabled whilst the molecule is being transformed or manipulated, and only January 2001 29 RASMOL(1) RASMOL(1) enabled once an appropiate viewpoint is selected, to provide a greater impression of depth. SSeett SSllaabbMMooddee The RasMol ssllaabbmmooddee parameter controls the render- ing method of objects cut by the slabbing (z-clip- ping) plane. Valid slabmode parameters are "reject", "half", "hollow", "solid" and "section". SSeett SSoollvveenntt The RasMol sseett ssoollvveenntt command is used to control the behaviour of the RasMol ddoottss command. Depending upon the value of the ssoollvveenntt parameter, the ddoottss command either generates a van der Waals' or a sol- vent accessible surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol rraaddiiuuss parameter. The command sseett ssoollvveenntt ffaallssee,, the default value, indicates that a van der Waals' sur- face should be generated and resets the value of rraaddiiuuss to zero. The command sseett ssoollvveenntt ttrruuee indi- cates that a 'Connolly' or 'Richards' solvent accessible surface should be drawn and sets the rraaddiiuuss parameter, the solvent radius, to 1.2 Angstroms (or 300 RasMol units). SSeett SSppeeccuullaarr The RasMol sseett ssppeeccuullaarr command enables and dis- ables the display of specular highlights on solid objects drawn by RasMol. Specular highlights appear as white reflections of the light source on the surface of the object. The current RasMol implemen- tation uses an approximation function to generate this highlight. The specular highlights on the surfaces of solid objects may be altered by using the specular reflection coefficient, which is altered using the RasMol sseett ssppeeccppoowweerr command. SSeett SSppeeccPPoowweerr The ssppeeccppoowweerr parameter determines the shininess of solid objects rendered by RasMol. This value between 0 and 100 adjusts the reflection coeffi- cient used in specular highlight calculations. The specular highlights are enabled and disabled by the RasMol sseett ssppeeccuullaarr command. Values around 20 or 30 produce plastic looking surfaces. High values rep- resent more shiny surfaces such as metals, while lower values produce more diffuse/dull surfaces. January 2001 30 RASMOL(1) RASMOL(1) SSeett SSSSBBoonnddss The RasMol ssssbboonnddss parameter determines whether disulphide bridges are drawn between the sulphur atoms in the sidechain (the default) or between the alpha carbon atoms in the backbone of the cysteines residues. The actual display of disulphide bridges is controlled by the ssssbboonnddss command. Drawing disulphide bridges between alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as bbaacckkbboonnee,, rriibbbboonnss or ssttrraannddss.. This parameter is similar to the Ras- Mol hhbboonnddss parameter. SSeett SStteerreeoo The RasMol sseett sstteerreeoo parameter controls the sepa- ration between the left and right images. Turning stereo on and off doesn't reposition the centre of the molecule. Stereo viewing of a molecule may be turned on (and off) either by selecting SStteerreeoo from the OOppttiioonnss menu, or by typing the commands sstteerreeoo oonn or sstteerreeoo ooffff.. The separation angle between the two views may be adjusted with the sseett sstteerreeoo [[--]] <> command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. Currently, stereo viewing is not supported in vveecc-- ttoorr PPoossttSSccrriipptt output files. SSeett SSttrraannddss The RasMol ssttrraannddss parameter controls the number of parallel strands that are displayed in the ribbon representations of proteins. The permissible values for this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The number of strands is con- stant for all ribbons being displayed. However, the ribbon width (the separation between strands) may be controlled on a residue by residue basis using the RasMol rriibbbboonnss command. SSeett TTrraannssppaarreenntt The RasMol ttrraannssppaarreenntt parameter controls the writ- ing of transparent GIFs by the wwrriittee ggiiff <> command. This may be controlled by the sseett ttrraannss-- ppaarreenntt oonn and sseett ttrraannssppaarreenntt ooffff commands. SSeett UUnniittCCeellll The RasMol uunniittcceellll parameter controls the display January 2001 31 RASMOL(1) RASMOL(1) of the crystallographic unit cell on the current display. The crystal cell is only enabled if the appropriate crystal symmetry information is con- tained in the PDB, CIF or mmCIF data file. The Ras- Mol command sshhooww ssyymmmmeettrryy display details of the crystal's space group and unit cell axes. The sseett uunniittcceellll command is similar to the commands sseett aaxxeess and sseett bboouunnddbbooxx that display orthogonal coor- dinate axes and the bounding box, respectively. SSeett VVeeccttPPSS The RasMol vveeccttppss parameter is use to control the way in which the RasMol wwrriittee command generates vector PostScript output files. The command sseett vveeccttppss oonn enables the use of black outlines around spheres and cylinder bonds producing "cartoon-like" high resolution output. However, the current imple- mentation of RasMol incorrectly cartoons spheres that are intersected by more than one other sphere. Hence "ball and stick" models are rendered cor- rectly but not large spacefilling spheres models. Cartoon outlines can be disabled, the default, by the command sseett vveeccttppss ooffff.. SSeett WWrriittee The RasMol wwrriittee parameter controls the use of the ssaavvee and wwrriittee commands within scripts, but it may only be executed from the command line. By default, this value is ffaallssee,, prohibiting the gen- eration of files in any scripts executed at start- up (such as those launched from a WWW browser). However, animators may start up RasMol interac- tively: type sseett wwrriittee oonn and then execute a script to generate each frame using the source command. AATTOOMM EEXXPPRREESSSSIIOONNSS RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions are composed of either primitive expressions, predefined sets, comparison operators, wwiitthhiinn expressions, or logical (boolean) combinations of the above expression types. The logical operators allow complex queries to be con- structed out of simpler ones using the standard boolean connectives aanndd,, oorr and nnoott.. These may be abbreviated by the symbols "&", "|" and "!", respectively. Parentheses (brackets) may be used to alter the precedence of the operators. For convenience, a comma may also be used for boolean disjunction. The atom expression is evaluated for each atom, hence January 2001 32 RASMOL(1) RASMOL(1) pprrootteeiinn aanndd bbaacckkbboonnee selects protein backbone atoms, not the protein and [nucleic] acid backbone atoms! PPrriimmiittiivvee EExxpprreessssiioonnss RasMol primitive expressions are the fundamental building blocks of atom expressions. There are two types of primitive expression. The first type is used to identify a given residue number or range of residue numbers. A single residue is identified by its number (position in the sequence), and a range is specified by lower and upper bounds separated by a hyphen character. For example sseelleecctt 55,,66,,77,,88 is also sseelleecctt 55--88.. Note that this selects the given residue numbers in all macromolecule chains. The second type of primitive expression specifies a sequence of fields that must match for a given atom. The first part specifies a residue (or group of residues) and an optional second part specifies the atoms within those residues. The first part consists of a residue name, optionally followed by a residue number and/or chain identifier. The second part consists of a period character fol- lowed by an atom name. An atom name may be up to four alphabetic or numeric characters. An optional semicolon followed by an alternate conformation identifier may be appended. An optional slash fol- lowed by a model number may also be appended. An asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard. CCoommppaarriissoonn OOppeerraattoorrss Parts of a molecule may also be distinguished using equality, inequality and ordering operators on their properties. The format of such comparison expression is a property name, followed by a com- parison operator and then an integer value. The atom properties that may be used in RasMol are aattoommnnoo for the atom serial number, eelleemmnnoo for the atom's atomic number (element), rreessnnoo for the residue number, rraaddiiuuss for the spacefill radius in RasMol units (or zero if not represented as a sphere) and tteemmppeerraattuurree for the PDB isotropic tem- perature value. The equality operator is denoted either "=" or "==". The inequality operator as either "<>", "!=" or "/=". The ordering operators are "<" for less January 2001 33 RASMOL(1) RASMOL(1) than, "<=" for less than or equal to, ">" for greater than, and ">" for greater than or equal to. WWiitthhiinn EExxpprreessssiioonnss A RasMol wwiitthhiinn expression allows atoms to be selected on their proximity to another set of atoms. A wwiitthhiinn expression takes two parameters separated by a comma and surrounded by parentheses. The first argument is an integer value called the "cut-off" distance of the within expression and the second argument is any valid atom expression. The cut-off distance is expressed in either integer RasMol units or Angstroms containing a decimal point. An atom is selected if it is within the cut-off distance of any of the atoms defined by the second argument. This allows complex expressions to be constructed containing nested wwiitthhiinn expres- sions. For example, the command sseelleecctt wwiitthhiinn((33..22,,bbaacckk-- bboonnee)) selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. WWiitthhiinn expressions are particularly useful for selecting the atoms around an active site. PPrreeddeeffiinneedd SSeettss RasMol atom expressions may contain predefined sets. These sets are single keywords that represent portions of a molecule of interest. Predefined sets are often abbreviations of primitive atom expressions. In some cases the use of predefined sets allows selection of areas of a molecule that could not otherwise be distinguished. A list of the currently predefined sets is given below. In addition to the sets listed here, RasMol also treats element names (and their plurals) as prede- fined sets containing all atoms of that element type, i.e. the command sseelleecctt ooxxyyggeenn is equivalent to the command sseelleecctt eelleemmnnoo==88.. PPrreeddeeffiinneedd SSeettss AATT SSeett This set contains the atoms in the complementary nucleotides adenosine and thymidine (A and T, respectively). All nucleotides are classified as either the set aatt or the set ccgg This set is equiva- lent to the RasMol atom expressions aa,,tt,, and nnuucclleeiicc aanndd nnoott ccgg.. AAcciiddiicc SSeett The set of acidic amino acids. These are the January 2001 34 RASMOL(1) RASMOL(1) residue types Asp and Glu. All amino acids are classified as either aacciiddiicc,, bbaassiicc oorr nneeuuttrraall.. This set is equivalent to the RasMol atom expres- sions aasspp,, gglluu and aammiinnoo aanndd nnoott ((bbaassiicc oorr nneeuu-- ttrraall)).. AAccyycclliicc SSeett The set of atoms in amino acids not containing a cycle or ring. All amino acids are classified as either ccyycclliicc or aaccyycclliicc.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott ccyycclliicc.. AAlliipphhaattiicc SSeett This set contains the aliphatic amino acids. These are the amino acids Ala, Gly, Ile, Leu and Val. This set is equivalent to the RasMol atom expres- sion aallaa,, ggllyy,, iillee,, lleeuu,, vvaall.. AAllpphhaa SSeett The set of alpha carbons in the protein molecule. This set is approximately equivalent to the RasMol atom expression **..CCAA.. This command should not be confused with the predefined set hheelliixx which con- tains the atoms in the amino acids of the protein's alpha helices. AAmmiinnoo SSeett This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the protein from the nucleic acid and heterogeneous atoms in the current molecule database. AArroommaattiicc SSeett The set of atoms in amino acids containing aromatic rings. These are the amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings all mem- bers of this set are member of the predefined set ccyycclliicc.. This set is equivalent to the RasMol atom expressions hhiiss,, pphhee,, ttrrpp,, ttyyrr and ccyycclliicc aanndd nnoott pprroo.. BBaacckkbboonnee SSeett This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O backbone of pro- teins, and the atoms of the sugar phosphate back- bone of nucleic acids. Use the RasMol predefined sets pprrootteeiinn and nnuucclleeiicc to distinguish between the two forms of backbone. Atoms in nucleic acids and January 2001 35 RASMOL(1) RASMOL(1) proteins are either bbaacckkbboonnee or ssiiddeecchhaaiinn.. This set is equivalent to the RasMol expression ((pprrootteeiinn oorr nnuucclleeiicc)) aanndd nnoott ssiiddeecchhaaiinn.. The predefined set mmaaiinncchhaaiinn is synonymous with the set bbaacckkbboonnee.. BBaassiicc SSeett The set of basic amino acids. These are the residue types Arg, His and Lys. All amino acids are classified as either aacciiddiicc,, bbaassiicc or nneeuuttrraall.. This set is equivalent to the RasMol atom expres- sions aarrgg,, hhiiss,, llyyss and aammiinnoo aanndd nnoott ((aacciiddiicc oorr nneeuuttrraall)).. BBoonnddeedd SSeett This set contain all the atoms in the current molecule database that are bonded to at least one other atom. BBuurriieedd SSeett This set contains the atoms in those amino acids that tend (prefer) to be buried inside protein, away from contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent accessibility for the current pro- tein. All amino acids are classified as either ssuurrffaaccee or bbuurriieedd.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott ssuurrffaaccee.. CCGG SSeett This set contains the atoms in the complementary nucleotides cytidine and guanosine (C and G, respectively). All nucleotides are classified as either the set aatt or the set ccgg This set is equiva- lent to the RasMol atom expressions cc,,gg and nnuucclleeiicc aanndd nnoott aatt.. CChhaarrggeedd SSeett This set contains the charged amino acids. These are the amino acids that are either aacciiddiicc or bbaassiicc.. Amino acids are classified as being either cchhaarrggeedd or nneeuuttrraall.. This set is equivalent to the RasMol atom expressions aacciiddiicc oorr bbaassiicc and aammiinnoo aanndd nnoott nneeuuttrraall.. CCyycclliicc SSeett The set of atoms in amino acids containing a cycle or rings. All amino acids are classified as either January 2001 36 RASMOL(1) RASMOL(1) ccyycclliicc or aaccyycclliicc.. This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set aarroommaattiicc are members of this set. The only cyclic but non-aromatic amino acid is proline. This set is equivalent to the RasMol atom expressions hhiiss,, pphhee,, pprroo,, ttrrpp,, ttyyrr and aarroo-- mmaattiicc oorr pprroo and aammiinnoo aanndd nnoott aaccyycclliicc.. CCyyssttiinnee SSeett This set contains the atoms of cysteine residues that form part of a disulphide bridge, i.e. half cystines. RasMol automatically determines disul- phide bridges, if neither the predefined set ccyyss-- ttiinnee nor the RasMol ssssbboonnddss command have been used since the molecule was loaded. The set of free cys- teines may be determined using the RasMol atom expression ccyyss aanndd nnoott ccyyssttiinnee.. HHeelliixx SSeett This set contains all atoms that form part of a protein alpha helix as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol ssttrruuccttuurree command. This predefined set should not be confused with the predefined set aallpphhaa which contains the alpha car- bon atoms of a protein. HHeetteerroo SSeett This set contains all the heterogeneous atoms in the molecule. These are the atoms described by HET- ATM entries in the PDB file. These typically con- tain water, cofactors and other solvents and lig- ands. All hheetteerroo atoms are classified as either lliiggaanndd or ssoollvveenntt atoms. These heterogeneous ssooll-- vveenntt atoms are further classified as either wwaatteerr or iioonnss.. HHyyddrrooggeenn SSeett This predefined set contains all the hydrogen, deu- terium and tritium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression eelleemmnnoo==11.. HHyyddrroopphhoobbiicc SSeett This set contains all the hydrophobic amino acids. January 2001 37 RASMOL(1) RASMOL(1) These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino acids are classified as either hhyyddrroopphhoobbiicc or ppoollaarr.. This set is equiv- alent to the RasMol atom expressions aallaa,, lleeuu,, vvaall,, iillee,, pprroo,, pphhee,, mmeett,, ttrrpp and aammiinnoo aanndd nnoott ppoollaarr.. IIoonnss SSeett This set contains all the heterogeneous phosphate and sulphate ions in the current molecule data file. A large number of these ions are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hheetteerroo atoms are classified as either lliiggaanndd or ssoollvveenntt atoms. All ssoollvveenntt atoms are classified as either wwaatteerr or iioonnss.. LLaarrggee SSeett All amino acids are classified as either ssmmaallll,, mmeeddiiuumm or llaarrggee.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott ((ssmmaallll oorr mmeeddiiuumm)).. LLiiggaanndd SSeett This set contains all the heterogeneous cofactor and ligand moieties that are contained in the cur- rent molecule data file. This set is defined to be all hheetteerroo atoms that are not ssoollvveenntt atoms. Hence this set is equivalent to the RasMol atom expres- sion hheetteerroo aanndd nnoott ssoollvveenntt.. MMeeddiiuumm SSeett All amino acids are classified as either ssmmaallll,, mmeeddiiuumm or llaarrggee.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott ((llaarrggee oorr ssmmaallll)).. NNeeuuttrraall SSeett The set of neutral amino acids. All amino acids are classified as either aacciiddiicc,, bbaassiicc or nneeuuttrraall.. This set is equivalent to the RasMol atom expres- sion aammiinnoo aanndd nnoott ((aacciiddiicc oorr bbaassiicc)).. NNuucclleeiicc SSeett The set of all atoms in nucleic acids, which con- sists of the four nucleotide bases adenosine, cyti- dine, guanosine and thymidine (A, C, G and T, respectively). All neucleotides are classified as January 2001 38 RASMOL(1) RASMOL(1) either ppuurriinnee or ppyyrriimmiiddiinnee.. This set is equiva- lent to the RasMol atom expressions aa,,cc,,gg,,tt and ppuurriinnee oorr ppyyrriimmiiddiinnee.. The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are also rec- ognized as members of this set. PPoollaarr SSeett This set contains the polar amino acids. All amino acids are classified as either hhyyddrroopphhoobbiicc or ppoollaarr.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott hhyyddrroopphhoobbiicc.. PPrrootteeiinn SSeett The set of all atoms in proteins. This consists of the RasMol predefined set aammiinnoo and common post- translation modifications. PPuurriinnee SSeett The set of purine nucleotides. These are the bases adenosine and guanosine (A and G, respectively). All nucleotides are either ppuurriinneess or ppyyrriimmiiddiinneess.. This set is equivalent to the RasMol atom expres- sions aa,,gg and nnuucclleeiicc aanndd nnoott ppyyrriimmiiddiinnee.. PPyyrriimmiiddiinnee SSeett The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T, respec- tively). All nucleotides are either ppuurriinneess or ppyyrriimmiiddiinneess.. This set is equivalent to the RasMol atom expressions cc,,tt and nnuucclleeiicc aanndd nnoott ppuurriinnee.. SSeelleecctteedd SSeett This set contains the set of atoms in the currently selected region. The currently selected region is defined by the preceding sseelleecctt or rreessttrriicctt command and not the atom expression containing the sseelleecctteedd keyword. SShheeeett SSeett This set contains all atoms that form part of a protein beta sheet as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol ssttrruuccttuurree command. January 2001 39 RASMOL(1) RASMOL(1) SSiiddeecchhaaiinn SSeett This set contains the functional sidechains of any amino acids and the base of each nucleotide. These are the atoms not part of the polypeptide N-C-C-O backbone of proteins or the sugar phosphate back- bone of nucleic acids. Use the RasMol predefined sets pprrootteeiinn and nnuucclleeiicc to distinguish between the two forms of sidechain. Atoms in nucleic acids and proteins are either bbaacckkbboonnee or ssiiddeecchhaaiinn.. This set is equivalent to the RasMol expression ((pprrootteeiinn oorr nnuucclleeiicc)) aanndd nnoott bbaacckkbboonnee.. SSmmaallll SSeett All amino acids are classified as either ssmmaallll,, mmeeddiiuumm or llaarrggee.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott ((mmeeddiiuumm oorr llaarrggee)).. SSoollvveenntt SSeett This set contains the solvent atoms in the molecule coordinate file. These are the heterogeneous water molecules, phosphate and sulphate ions. All hheetteerroo atoms are classified as either lliiggaanndd or ssoollvveenntt atoms. All ssoollvveenntt atoms are classified as either wwaatteerr or iioonnss.. This set is equivalent to the Ras- Mol atom expressions hheetteerroo aanndd nnoott lliiggaanndd and wwaatteerr oorr iioonnss.. SSuurrffaaccee SSeett This set contains the atoms in those amino acids that tend (prefer) to be on the surface of pro- teins, in contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent accessibility for the current pro- tein. All amino acids are classified as either ssuurrffaaccee or bbuurriieedd.. This set is equivalent to the RasMol atom expression aammiinnoo aanndd nnoott bbuurriieedd.. TTuurrnn SSeett This set contains all atoms that form part of a protein turns as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure deter- mination given in the PDB file if it exists. Oth- erwise, it uses the DSSP algorithm as used by the RasMol ssttrruuccttuurree command. WWaatteerr SSeett This set contains all the heterogeneous water January 2001 40 RASMOL(1) RASMOL(1) molecules in the current database. A large number of water molecules are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hheetteerroo atoms are classified as either lliiggaanndd or ssoollvveenntt atoms. The ssoollvveenntt atoms are further classified as either wwaatteerr or iioonnss.. SSeett SSuummmmaarryy The table below summarises RasMol's classification of the common amino acids. CCOOLLOOUURR SSCCHHEEMMEESS The RasMol ccoolloouurr command allows different objects (such as atoms, bonds and ribbon segments) to be given a speci- fied colour. Typically this colour is either a RasMol pre- defined colour name or an RGB triple. Additionally RasMol also supports aalltt,, aammiinnoo,, cchhaaiinn,, cchhaarrggee,, ccppkk,, ggrroouupp,, mmooddeell,, sshhaappeellyy,, ssttrruuccttuurree,, tteemmppeerraattuurree or uusseerr colour schemes for atoms, and hhbboonndd ttyyppee colour scheme for hydro- gen bonds and eelleeccttrroossttaattiicc ppootteennttiiaall colour scheme for dot surfaces. The 24 currently predefined colour names are Black, Blue, BlueTint, Brown, Cyan, Gold, Grey, Green, GreenBlue, GreenTint, HotPink, Magenta, Orange, Pink, PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue, Vio- let, White, Yellow and YellowTint If you frequently wish to use a colour not predefined, you can write a one-line script. For example, if you make the file ggrreeyy..ccooll containing the line, ccoolloouurr [[118800,,118800,,118800]] ##ggrreeyy,, then the command ssccrriipptt ggrreeyy..ccooll colours the cur- rently selected atom set grey. AAlltt CCoolloouurrss The RasMol aalltt (Alternate Conformer) colour scheme codes the base structure with one colour and applies a limited number of colours to each alter- nate conformer. In a RasMol built for 8-bit color systems, 4 colours are allowed for alternate con- formers. Otherwise, 8 colours are available. AAmmiinnoo CCoolloouurrss The RasMol aammiinnoo colour scheme colours amino acids according to traditional amino acid properties. The purpose of colouring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the sshhaappeellyy scheme. January 2001 41 RASMOL(1) RASMOL(1) CChhaaiinn CCoolloouurrss The RasMol cchhaaiinn colour scheme assigns each macro- molecular chain a unique colour. This colour scheme is particularly useful for distinguishing the parts of multimeric structure or the individual 'strands' of a DNA chain. CChhaaiinn can be selected from the RasMol CCoolloouurrss menu. CChhaarrggee CCoolloouurrss The RasMol cchhaarrggee colour scheme colour codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are coloured in blue (positive) and lower values coloured in red (negative). Rather than use a fixed scale this scheme determines the maximum and minimum values of the charge/tempera- ture field and interpolates from red to blue appro- priately. Hence, green cannot be assumed to be 'no net charge' charge. The difference between the cchhaarrggee and tteemmppeerraattuurree colour schemes is that increasing temperature val- ues proceed from blue to red, whereas increasing charge values go from red to blue. If the charge/temperature field stores reasonable values it is possible to use the RasMol ccoolloouurr ddoottss ppootteennttiiaall command to colour code a dot surface (generated by the ddoottss command) by electrostatic potential. CCPPKK CCoolloouurrss The RasMol ccppkk colour scheme is based upon the colours of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kultun. This colour scheme colours 'atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. The assignment of the most commonly used element types to colours is given below. GGrroouupp CCoolloouurrss The RasMol ggrroouupp colour scheme colour codes residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue through green, yellow and orange to red. Hence the N terminus of proteins and 5' terminus of nucleic acids are coloured red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. If a chain has a large number of heterogeneous molecules associated with it, the January 2001 42 RASMOL(1) RASMOL(1) macromolecule may not be drawn in the full 'range' of the spectrum. GGrroouupp can be selected from the RasMol CCoolloouurrss menu. If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may not be drawn in the full range of the spectrum. When RasMol performs group coloring it decides the range of colors it uses from the residue numbering given in the PDB file. Hence the lowest residue number is displayed in blue and the highest residue number is displayed as red. Unfortunately, if a PDB file contains a large number of heteroatoms, such as water molecules, that occupy the high residue numbers, the protein is displayed in the blue-green end of the spectrum and the waters in the yellow- red end of the spectrum. This is aggravated by there typically being many more water molecules than amino acid residues. The solution to this problem is to use the command sseett hheetteerroo ooffff before applying the group color scheme. This can also be achieved by toggling HHeetteerroo AAttoommss on the OOppttiioonnss menu before selecting GGrroouupp on the CCoolloouurr menu. This command instructs RasMol to only use non-het- ero residues in the group color scaling. NNMMRR MMooddeell CCoolloouurrss The RasMol mmooddeell colour scheme codes each NMR model with a distinct colour. The NMR model number is taken as a numeric value. High values are coloured in blue and lower values coloured in red. Rather than use a fixed scale this scheme determines the maximum value of the NMR model number and interpo- lates from red to blue appropriately. SShhaappeellyy CCoolloouurrss The RasMol sshhaappeellyy colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The sshhaappeellyy colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the aammiinnoo colour scheme. SSttrruuccttuurree CCoolloouurrss The RasMol ssttrruuccttuurree colour scheme colours the molecule by protein secondary structure. Alpha helices are coloured magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255] and all other residues are coloured white. The secondary January 2001 43 RASMOL(1) RASMOL(1) structure is either read from the PDB file (HELIX, SHEET and TURN records), if available, or deter- mined using Kabsch and Sander's DSSP algorithm. The RasMol ssttrruuccttuurree command may be used to force DSSP's structure assignment to be used. TTeemmppeerraattuurree CCoolloouurrss The RasMol tteemmppeerraattuurree colour scheme colour codes each atom according to the anisotropic temperature (beta) value stored in the PDB file. Typically this gives a measure of the mobility/uncertainty of a given atom's position. High values are coloured in warmer (red) colours and lower values in colder (blue) colours. This feature is often used to asso- ciate a "scale" value [such as amino acid variabil- ity in viral mutants] with each atom in a PDB file, and colour the molecule appropriately. The difference between the tteemmppeerraattuurree and cchhaarrggee colour schemes is that increasing temperature val- ues proceed from blue to red, whereas increasing charge values go from red to blue. UUsseerr CCoolloouurrss The RasMol uusseerr colour scheme allows RasMol to use the colour scheme stored in the PDB file. The colours for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon's Raster3D program. HHBBoonndd TTyyppee CCoolloouurrss The RasMol ttyyppee colour scheme applies only to hydrogen bonds, hence is used in the command ccoolloouurr hhbboonnddss ttyyppee.. This scheme colour codes each hydro- gen bond according to the distance along a protein chain between hydrogen bond donor and acceptor. This schematic representation was introduced by Belhadj-Mostefa and Milner-White. This representa- tion gives a good insight into protein secondary structure (hbonds forming alpha helices appear red, those forming sheets appear yellow and those form- ing turns appear magenta). PPootteennttiiaall CCoolloouurrss The RasMol ppootteennttiiaall colour scheme applies only to dot surfaces, hence is used in the command ccoolloouurr ddoottss ppootteennttiiaall.. This scheme colours each currently displayed dot by the electrostatic potential at that point in space. This potential is calculated using Coulomb's law taking the temperature/charge January 2001 44 RASMOL(1) RASMOL(1) field of the input file to be the charge assocated with that atom. This is the same interpretation used by the ccoolloouurr cchhaarrggee command. Like the cchhaarrggee colour scheme low values are blue/white and high values are red. AAmmiinnoo AAcciidd CCooddeess The following table lists the names, single letter and three letter codes of each of the amino acids. BBoooolleeaannss A boolean parameter is a truth value. Valid boolean values are 'true' and used by RasMol to either enable or disable a representation or option. FFIILLEE FFOORRMMAATTSS PPrrootteeiinn DDaattaa BBaannkk FFiilleess If you do not have the PDB documentation, you may find the following summary of the PDB file format useful. The Protein Data Bank is a computer-based archival database for macromolecular structures. The database was established in 1971 by Brookhaven National Laboratory, Upton, New York, as a public domain repository for resolved crystallographic structures. The Bank uses a uniform format to store atomic coordinates and partial bond connectivities as derived from crystallographic studies. In 1999 the Protein Data Bank moved to the Research Collab- oratory for Structural Biology. PDB file entries consist of records of 80 charac- ters each. Using the punched card analogy, columns 1 to 6 contain a record-type identifier, the columns 7 to 70 contain data. In older entries, columns 71 to 80 are normally blank, but may con- tain sequence information added by library manage- ment programs. In new entries conforming to the 1996 PDB format, there is other information in those columns. The first four characters of the record identifier are sufficient to identify the type of record uniquely, and the syntax of each record is independent of the order of records within any entry for a particular macromolecule. The only record types that are of major interest to the RasMol program are the ATOM and HETATM records which describe the position of each atom. ATOM/HET- ATM records contain standard atom names and residue abbreviations, along with sequence identifiers, coordinates in Angstrom units, occupancies and thermal motion factors. The exact details are given January 2001 45 RASMOL(1) RASMOL(1) below as a FORTRAN format statement. The "fmt" column indicates use of the field in all PDB for- mats, in the 1992 and earlier formats or in the 1996 and later formats. Residues occur in order starting from the N-termi- nal residue for proteins and 5'-terminus for nucleic acids. If the residue sequence is known, certain atom serial numbers may be omitted to allow for future insertion of any missing atoms. Within each residue, atoms are ordered in a standard man- ner, starting with the backbone (N-C-C-O for pro- teins) and proceeding in increasing remoteness from the alpha carbon, along the side chain. HETATM records are used to define post-transla- tional modifications and cofactors associated with the main molecule. TER records are interpreted as breaks in the main molecule's backbone. If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN, CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as the name, database code, revision date and classi- fication of the molecule are extracted from HEADER and COMPND records, initial secondary structure assignments are taken from HELIX, SHEET and TURN records, and the end of the file may be indicated by an END record. RRaassMMooll IInntteerrpprreettaattiioonn ooff PPDDBB ffiieellddss Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are also assumed to be pseudo atoms or position markers. When a data file contains an NMR structure, multi- ple conformations may be placed in a single PDB file delimited by pairs of MODEL and ENDMDL records. RasMol displays all the NMR models con- tained in the file. Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP" are considered pseudonyms for water "HOH". The residue name "D20" is consider heavy water "DOD". The residue name "SUL" is con- sidered a sulphate ion "SO4". The residue name "CPR" is considered to be cis-proline and is trans- lated as "PRO". The residue name "TRY" is consid- ered a pseudonym for tryptophan "TRP". RasMol uses the HETATM fields to define the sets January 2001 46 RASMOL(1) RASMOL(1) hetero, water, solvent and ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or aliased to one of these names by the preceding rules) is considered a solvent and is considered to be defined by a HETATM field. RasMol only respects CONECT connectivity records in PDB files containing fewer than 256 atoms. This is explained in more detail in the section on deter- mining molecule connectivity. CONECT records that define a bond more than once are interpreted as specifying the bond order of that bond, i.e. a bond specified twice is a double bond and a bond speci- fied three (or more) times is a triple bond. This is not a standard PDB feature. PPDDBB CCoolloouurr SScchheemmee SSppeecciiffiiccaattiioonn RasMol also accepts the supplementary COLO record type in the PDB files. This record format was introduced by David Bacon's Raster3D program for specifying the colour scheme to be used when ren- dering the molecule. This extension is not cur- rently supported by the PDB. The COLO record has the same basic record type as the ATOM and HETATM records described above. Colours are assigned to atoms using a matching pro- cess. The Mask field is used in the matching pro- cess as follows. First RasMol reads in and remem- bers all the ATOM, HETATM and COLO records in input order. When the user-defined ('User') colour scheme is selected, RasMol goes through each remembered ATOM/HETATM record in turn, and searches for a COLO record that matches in all of columns 7 through 30. The first such COLO record to be found determines the colour and radius of the atom. Note that the Red, Green and Blue components are in the same positions as the X, Y, and Z components of an ATOM or HETA record, and the van der Waals radius goes in the place of the Occupancy. The Red, Green and Blue components must all be in the range 0 to 1. In order that one COLO record can provide colour and radius specifications for more than one atom (e.g. based on residue, atom type, or any other criterion for which labels can be given somewhere in columns 7 through 30), a 'don't-care' character, the hash mark "#" (number or sharp sign) is used. This character, when found in a COLO record, matches any character in the corresponding column in a ATOM/HETATM record. All other characters must January 2001 47 RASMOL(1) RASMOL(1) match identically to count as a match. As an exten- sion to the specification, any atom that fails to match a COLO record is displayed in white. MMuullttiippllee NNMMRR MMooddeellss RasMol loads all of the NMR models from a PDB file no matter which command is used: llooaadd ppddbb <> or llooaadd nnmmrrppddbb <> Once multiple NMR conformations have been loaded they may be manipulated with the atom expression extensions described in PPrriimmiittiivvee EExxpprreessssiioonnss.. In particular, the command rreessttrriicctt **//11 will restrict the display to the first model only. CCIIFF aanndd mmmmCCIIFF FFoorrmmaatt FFiilleess CIF is the IUCr standard for presentation of small molecules and mmCIF is intended as the replacement for the fixed-field PDB format for presentation of macromolecular structures. RasMol can accept data sets in either format. There are many useful sites on the World Wide Web where information tools and software related to CIF, mmCIF and the PDB can be found. The following are good starting points for exploration: The International Union of Crystallography (IUCr) provides access to software, dictionaries, policy statements and documentation relating to CIF and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/) with many mirror sites. The Nucleic Acid Database Project provides access to its entries, software and documentation, with an mmCIF page giving access to the dictionary and mmCIF software tools at Rutgers University, New Jersey, USA (http://ndbserver.rut- gers.edu/NDB/mmcif) with many mirror sites. This version of RasMol restricts CIF or mmCIF tag values to essentially the same conventions as are used for the fixed-field PDB format. Thus chain identifiers and alternate conformation identifiers are limited to a single character, atom names are limited to 4 characters, etc. RasMol interprets the following CIF and mmCIF tags: A search is made through multiple data blocks for the desired tags, so a single dataset may be composed from multiple data blocks, but multiple data sets may not be stacked in the same file. January 2001 48 RASMOL(1) RASMOL(1) MMAACCHHIINNEE--SSPPEECCIIFFIICC SSUUPPPPOORRTT In the following sections, support for MMoonnoocchhrroommee XX--WWiinn-- ddoowwss,, TTccll//TTkk IIPPCC,, UUNNIIXX ssoocckkeettss bbaasseedd IIPPCC,, CCoommppiilliinngg RRaassWWiinn wwiitthh BBoorrllaanndd aanndd MMeettrrooWWeerrkkss are described. MMoonnoocchhrroommee XX--WWiinnddoowwss SSuuppppoorrtt RasMol supports the many monochrome UNIX worksta- tions typically found in academia, such as low-end SUN workstations and NCD X-terminals. The X11 ver- sion of RasMol (when compiled in 8 bit mode) now detects black and white X-Windows displays and enables dithering automatically. The use of run- time error diffusion dithering means that all dis- play modes of RasMol are available when in monochrome mode. For best results, users should experiment with the set ambient command to ensure the maximum contrast in resulting images. TTccll//TTkk IIPPCC ssuuppppoorrtt Version 4 of Tk graphics library changed the proto- col used to communicate between Tk applications. RasMol version 2.6 was modified such that it could communicate with both this new protocol and the previous version 3 protocol supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only communicate with other 3.x applications and Tcl/Tk 4.x applications with other 4.x applications, these changes allow RasMol to communicate between pro- cesses with both protocols (potentially concur- rently). UUNNIIXX ssoocckkeettss bbaasseedd IIPPCC The UNIX implementation of RasMol supports BSD- style socket communication. An identical socket mechanism is also being developed for VMS, Apple Macintosh and Microsoft Windows systems. This should allow RasMol to interactively display results of a computation on a remote host. The cur- rent protocol acts as a TCP/IP server on port 21069 that executes command lines until either the com- mand eexxiitt or the command qquuiitt is typed. The command exit from the RasMol server, the command qquuiitt both disconnects the current session and terminates Ras- Mol. This functionality may be tested using the UNIX command tteellnneett <> 2211006699.. CCoommppiilliinngg RRaassWWiinn wwiitthh BBoorrllaanndd aanndd MMeettrrooWWeerrkkss A number of changes were made to the source code in the transition from version 2.5 to 2.6 to allow the Microsoft Windows version of RasMol to compile January 2001 49 RASMOL(1) RASMOL(1) using the Borland C/C++ compiler. These fixes include name changes for the standard library and special code to avoid a bug in _fmemset. Addi- tional changes were made in the transition from 2.6 to 2.7 to allow compilation with the MetroWerks compilers. BBIIBBLLIIOOGGRRAAPPHHYY MMoolleeccuullaarr GGrraapphhiiccss [1] Nelson Max, "Computer Representation of Molecu- lar Surfaces", IEEE Computer Graphics and Applica- tions, pp.21-29, August 1983. [2] Arthur M. Lesk, "Protein Architecture: A Prac- tical Approach", IRL Press Publishers, 1991. MMoolleeccuullaarr GGrraapphhiiccss PPrrooggrraammss [3] Per J. Kraulis, "MOLSCRIPT: A Program to Pro- duce both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography, Vol.24, pp.946-950, 1991. [4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering Space-Filling Molecule Pic- tures", Journal of Molecular Graphics, Vol.6, No.4, pp.219-220, December 1988. [5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool for Scientific Communica- tion", Protein Science, Vol.1, No.1,pp.3-9, January 1992. [6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography, Vol.24, pp.958-961, 1991. [7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. Ferrin and Robert Langridge, "Conic: A Fast Renderer for Space-Filling Molecules with Shadows", Journal of Molecular Graphics, Vol.9, No.4, pp.230-236, December 1991. MMoolleeccuullaarr BBiioollooggyy AAllggoorriitthhmmss [8] Wolfgang Kabsch and Christian Sander, "Dictio- nary of Protein Secondary Structure: Pattern Recog- nition of Hydrogen-Bonded and Geometrical Fea- tures", Biopolymers, Vol.22, pp.2577-2637, 1983. [9] Michael L. Connolly, "Solvent-Accessible Sur- faces of Proteins and Nucleic Acids", Science, Vol.221, No.4612, pp.709-713, August 1983. January 2001 50 RASMOL(1) RASMOL(1) [10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White, "Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins", Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991. [11] Mike Carson, "Ribbon Models of Macro- molecules", Journal of Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987. [12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of Proteins", Journal of Molecu- lar Graphics, Vol.4, No.2, pp.121-122, June 1986. [13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of Effective van der Waals Atomic Con- tact Radii for Proteins and Peptides", Proteins: Structure, Functions and Genetics, Vol.2, pp.330-339,1987. GGrraapphhiiccss AAllggoorriitthhmmss [14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics: Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990. [15] J. Cleary and G. Wyvill, "Analysis of an Algo- rithm for Fast Ray Tracing using Uniform Space Sub- division", The Visual Computer, Vol.4, pp.65-83, 1988. [16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM SIGGRAPH, pp.282-285, 1978. [17] Jean-Michel Cense, "Exact Visibility Calcula- tion for Space-Filling Molecular Models", Journal of Molecular Graphics, Vol.9, No.3, pp.191-193, September 1991. [18] Chris Schafmeister, "Fast Algorithm for Gener- ating CPK Images on Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4, pp.201-206, December 1990. [19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the Representation of Molecular Sur- faces", Journal of Molecular Graphics, Vol.5, No.3, pp.167-169, September 1987. FFiillee FFoorrmmaattss [20] Frances C. Bernstein et al., "The Protein Data Bank: A Computer-Based Archival File for Macro- molecular Structures", Journal of Molecular Biol- ogy, Vol.112, pp.535-542, 1977. January 2001 51 RASMOL(1) RASMOL(1) [21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I. Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description of Several Chemical File Formats Used by Computer Pro- grams Developed at Molecular Design Limited", Jour- nal of Chemical Information and Computer Sciences, Vol.32, No.3, pp.244-255, 1992. [22] Adobe Systems Inc., "PostScript Language Ref- erence Manual", Addison-Wesley Publishers, Reading, Mass., 1985. [23] Philip E. Bourne et al., "The Macromolecular Crystallographic Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590. [24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data Transfer and Archiving", Jour- nal of Chemical Information and Computer Sciences, Vol. 31, 326-333, 1991. SSEEEE AALLSSOO The RasMol User Manual! AAUUTTHHOORR 1992-1998 by Roger Sayle 1998-2001 by Herbert J. Bernstein (yaya@bernstein-plus-sons.com) January 2001 52