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A molecular Visualisation Program

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RasMol v2.5

A Molecular Visualisation Program

Roger Sayle

Biomolecular Structure

Glaxo Research and Development

Greenford, Middlesex, UK.

Last Updated 28th October 1994

Copyright (C) 1992,1993,1994 by Roger Sayle (rasmol@ggr.co.uk)

All rights reserved. Use of copyright notice does not imply publication or disclosure. The information supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier.

This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose other than the purchaser's personal use without contacting the author.

This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. The author, nor his employer, shall not be liable, in whole or in part, for any claims or damages arising from such use, including death, bancruptcy or outbreak of war.

The Graphics Interchange Format is the copyright property and Service Mark of Compuserve Incorporated.

Microsoft and MS-DOS are registered trademarks and Windows is a trademark of Microsoft Corporation.

Macintosh is a trademark and Apple is a registered trademark of Apple Computer Inc.

The X Window System is a trademark of the Massacheusetts Institute of Technology.

IBM is a registered trademark of International Business Machines Corporation.

OSF/Motif and Motif are trademarks of Open Software Foundation, Inc.

PostScript is a registered trademark of Adobe Systems Incorporated.

Alchemy and Sybyl are trademarks of Tripos Associates Inc.

VAX is a trademark of Digital Equipment Corporation.

ISIS is a trademark of Molecular Design Limited.


RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including SGI, sun4, sun3, sun386i, DEC, HP and E&S workstations, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM RS/6000, Cray, Sequent, VAX VMS (under DEC windows), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh and PowerMac. UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (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 molecular co-ordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Brookhaven Protein Databank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Centre's (MSC) XYZ (XMol) format and CHARMm format files. If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box. RasMol can read a prepared list of commands from a 'script' file (or via inter-process communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally, the rendered image may be written out in a variety of formats including either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.

RasMol has been developed at the University of Edinburgh's Biocomputing Research Unit and the BioMolecular Structure Department, Glaxo Research and Development, Greenford, U.K.

If you have any comments, questions, suggestions or complaints please do not hesitate to contact the author:

Roger Sayle, Email: ras32425@ggr.co.uk

Biomolecular Structure, rasmol@dcs.ed.ac.uk

Glaxo Research and Development,

Greenford Road, Greenford, Tel: (+44) (0)81 966 3567

Middlesex UB6 0HE. Fax: (+44) (0)81 966 4476




Running RasMol Under UNIX or VMS

To start RasMol from either the UNIX or VMS prompt, type the command 'rasmol'. This command can be followed by an optional filename. By default Immediately upon starting, the program displays the following message to identify the version number and display depth of the running program:

^ RasMol Molecular Renderer

Roger Sayle, October 1994

Version 2.5

[8bit version]

Immediately underneath this banner message, appears the program's command line prompt 'RasMol>'. If the program is being executed under the X Window System, the program determines the type of the display being used. If the screen has either an 8 bit or 24 bit colour frame buffer, RasMol creates another window, which is used to display menu options and the rendered images. If a suitable screen is not available, RasMol may only be used from the command line. Commands may be typed to manipulate the model, and to output the generated image to a raster file.

If the program is run under the X Window System environment with a suitable colour screen, RasMol creates an additional window to display the rendered molecule interactively, as it is manipulated. If RasMol is not run under the X Window system, the program displays the message 'No suitable display detected!'. RasMol may instructed not to display a graphics window by using the command line option "-nodisplay". This is particularly useful for using RasMol as a background or batch process.

It is possible to specify either a coordinate filename or a script filename or both on the UNIX/VMS command line. The format for specifying a script file to add the option "-script " to the command line. A molecule co-ordinate file may be specified by placing its name on the command line, optionally preceded by a file format option. If no format option is given, the specified co-ordinate file is assumed to be in PDB format. Valid format options include "-pdb", "-mdl", "-mol2", "-xyz", "-alchemy" and "-charmm", which correspond to Brookhaven, MDL Mol file, Sybyl Mol2, MSC's xyz, Alchemy and CHARMm formats respectively. If both a co-ordinate file and a script file are specified on the command line, the molecule is loaded first, then the script commands are applied to it. If either file is not found, the program displays the error message 'Error: File not found!' and the user is presented the RasMol prompt.

In order to leave RasMol, the user can type the command quit or exit at the RasMol prompt, and the program will return the user to the familiar unix prompt. Alternatively, if a prompt other than the main RasMol prompt is being displayed, the user may hit control-C (^C) to leave the program. The message '*** Quit ***' will be output to the terminal, before the usual unix prompt is redisplayed. The program may also be terminated by selecting the Quit menu option, on the bottom of the main menu.

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