www.OpenRasMol.org/FAQ.html
Free RasMol Download, RasMol 2.7.5 Download. There is nothing to install (except maybe java) and everything works on Windows, Mac OS X, and linux.
This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol. Login; Registration; Saved Software; Top Downloads. Easy Translator for Mac OS X. Swordfish for Mac OS X. The R Commander. Note: we are using Rasmol in MacOSX under X-windows. It needs to be launched by line-command as shown below. In Windows and Mac Classic you can launch Rasmol by double clicking either on the PDB file or on the Rasmol (Rasmac / Raswin) icon. TASK 1) Open the Rasmol program and a molecule at the same time.
| RasMol Manual |Frequently Asked Questions |RasMol 2.7 Series History |RasMol and OpenRasMol |
| Click Here to Make a Donation |
Molecular Graphics Visualisation Tool
RasMol is a program for molecular graphics visualisation originallydeveloped by Roger Sayle. This site is provided for the convenienceof users and software developers of open source versions of RasMol.In order to ensure continuing availability of source code anddocumentation most programs and documents on this siteare subject to copyright. This does not prevent you from usingthe open-source versions of RasMol, from making copies and changes,but prevents the creation of 'closed source' versionsout of the open source versions. Appropriate copyrights and licensesappear with the relevant sources and documents. SeeCopyright and NOTICEfor applicable Copyright and other Notices.The 'Frequently Asked Questions' (FAQ) document for OpenRasMol is derived in part from two FAQs posted to the web by Eric Martz athttp://www.umass.edu/microbio/rasmol/faq.htm,one FAQ by Roger Sayle, and one by Eric Martz. The portions of theFAQs from the Martz web site are included by permission of Eric Martz.Many of the questions in thisdocument are the same or similar to those in the earlier FAQs, but someof the answers are different. If all or part of an answer is identical to given by Roger Sayle or Eric Martz, we will put that portion in quote marks and indicate the attribution by '--RS' or '--EM'.
Some of the responses to questions come from the RasMol manual.
The original RasMol manual was created by Roger Sayle. In July 1996,Dr. Margaret Wong of the Chemistry Department, Swinburne Universityof Technology, Australia, made extensive revisions to the RasMol 2.5manual to accurately reflect the operation of RasMol 2.6. Eric Martzof the University of Massachusetts made further revisions. In May1997, William McClure of Carnegie Mellon University reorganized theHTML version of the manual into multiple sections which could bedownloaded quickly and added use of frames. Portions of the 2.7.1version of the RasMol manual were derived with permission fromWilliam McClure's version using Roger Sayle's rasmol.doc for?version 2.6.4 as the primary source. Changes have been made inAugust 2000 for RasMol version 2.7.2.
The RasMol documentation was adapted for RasTop by PhilippeValadon in August 2000.
Edited by Philippe Valadon
Edited by Herbert J. Bernstein and Frances C. Bernstein
Contents
What is this document?
This document is a compilation of questions about RasMol that either have been asked with some frequency, or which the authors of this document think mightinterest people who use RasMol.
Why won't the RasWin.exe I just downloaded run?
Many web browsers try to download RasWin.exe and its help filesas if they were ordinary text files. They are all binary files.In some cases, a browser can be convinced to do a binary downloadby holding down one of the shift keys (Alt, Opt, Shift, etc.), whileclicking on the download link. If that does not work, then youwill have to download gzipped files and unpack them under Windows.Sometimes your browser will be willing to download the gzippedfiles as binary files, but if that does not work, you will have toresort to the File Tranfer Protocol (FTP) client packaged withall copies of Windows.
I get the message 'No suitable display detected!'
This is a problem on the UNIX version of RasMol caused by one oftwo potential problems. The first is that your DISPLAYenvironment variable isn't set corrrectly or that you don't havepermission to display to the X Windows server. This can bechecked by testing whether it is possible to run any other X Windows program.The second problem is caused by a mismatch between the configured version of RasMol and the display depths available on the current X Windows server. This is most often the case when RasMol has beencompiled in 24/32bit mode (by defining THIRTYTWOBIT in either rasmol.hor Makefile). The 24/32bit mode indicates that RasMol should use3bytes/pixel (or 16 million simultaneous colours). If the currentX Windows server is unable to display this visual depth it reportsthe 'No suitable display' error. The visual depths supported by the current X Windows server can be reported by typing the 'xdpyinfo' command. To solve the problem, recompile RasMol withEIGHTBIT defined instead (i.e use one byte/pixel or 256 simultaneouscolours).
Note: that RasMol must be configured with EIGHTBIT for 1bit/pixel(monochrome) or 8bit/pixel displays, with SIXTEENBIT for 16bit/pixeldisplays and with THIRTYTWOBIT for either 24bit/pixel or 32bit/pixeldisplays.
--RSIn pactice on most UNIX systems, the fastest way to change thepixel bit depth after a 'xmkmf' has been done, is to edit thefile 'Makefile', commenting out the wrong definition (i.e. ofEIGHTBIT, SIXTEENBIT or THIRTYTWOBIT) and uncommenting theright definition. Then 'make clean' followed by 'make' shouldcorrect the problem.
Why are there such long headers on these web pages?
We regret the necessity for the long headers. They are part of the hoops wehave to jump through to keep OpenRasMol programs and RasMol 2.7 series of releases in particular available as 'open source' software.(Please see the web page on Copyrights and Notices)
Can RasMol be distributed freely, on CD-ROMs, andused freely even for commercial purposes?
Different versions of RasMol have had different rules forredistribution. The rules for the RasMol 2.7 series are intendedto allow redistribution on an 'open source' basis.The idea is to encourage distribution of RasMol and programsderived from RasMol provided source code and documentationremain available, and a few other sensible conditions areaccepted by the distributor.
Starting with RasMol release 2.7.3, RasMol may be distributedunder the GPL, one of the most popularopen source licenses.
The specific rules for all recent RasMol releases are given in the file NOTICE.
Does this mean I can't make a commercial graphics programbased on RasMol?
If what you mean by 'commercial' is that you want to distributebinary versions and keep the source code as a secret, no, you may not do that, but if what you mean by 'commercial' is that you wishto sell programs and services based on RasMol, that you certainly may do.Just remember that your new and wonderful program has to include or referenceall the original source code and documentation, including the fileNOTICE, which will allow other people to copyyour program. In other words the rules for distributing copies ofRasMol that you have taken advantage of will also apply to people whowish to make copes of your program.
A lot of people find it easy to work within this framework, but if youneed to do commerical development which does not fit the open sourcemodel, you may not make use of any substantial portion of theRasMol 2.7 series to develop your own product.
What is the relationship between RasMol, Linux and the GPL?
RasMol 2.7 runs quite nicely under Linux. There are pre-compiled binariesof the 2.7 series to run under Linux. Starting with the RasMol 2.7.3release, RasMol may be distributed under the GPL.However, earlier RasMol 2.7 releases are not coveredby the GPL. Those RasMol 2.7 releases have their own 'GPL-like' license (RASLIC, which carefully avoidscertain issues which, until recently, would have caused problems if we had used the GPL for those releases. Those problems havenow been resolved, and we can now use the GPL.
Is RasMol 'Year 2000 (Y2K) compliant'?
RasMol 2.6 and all prior versions are fully Y2K compliant with a singlecaveat. RasMol can read and write MDL Mol and Brookhaven PDB files, whichreserve only two characters for the year in a date field. RasMol ignoresthese fields and is therefore not affected by Y2K. However programsreading MDL Mol files generated by RasMol (or any other molecular graphicsprogram) may suffer if they process the date field.--RS
In addition, please note that we are now well past 31 December 1999, andthere has not been a single report of a Y2K-related RasMol failure.
Is RasMol 'Euro compliant'?
IT managers in the 'euro-zone' need to assure themselves thatall software they use will support the Euro by January 1, 2002.RasMol does not deal with currency, and therefore is effectively'Euro compliant'. However, most existing versions of RasMol usethe Latin-1 (ANSI), Macintosh, or MS Windows OEM characters sets,without explicit support for the Euro symbol, which might causeRasMol to be rejected in testing for 'Euro compliance' against standardsintended for financial software. If this proves to be a nuisance,please contact EuroCompliance@OpenRasMol.org
What are the definitive literature citations for RasMol?
The currently preferred literature reference to RasMol is: Roger Sayle and E. James Milner-White. 'RasMol: Biomolecular graphics for all', Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.--RS
In addition the best reference for the 2.7 series is:Herbert J. Bernstein, 'Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455.
Where can I get more molecule co-ordinate files?
In addition to the example files that are distributed with RasMol the major source of data files for RasMol isthe Protein Data Bank operated by the Research Collaboratory forBioinformatics (see http://www.rcsb.org/pdb). This is the mainrepository for all of the world's known 3D xray-crystallography andnuclear magnetic resonance (NMR) structures of proteins and nucleicacids. Currently (September 2000) over 13,000 are available from mirrorsites throughout the world (see http://www.rcsb.org/pdb/mirrors.htmlThe primary archive for three dimensional structures of small moleculesis the Cambridge Crystallographic Data Centre, with over 200,000 organic andmetal organic compounds (see http://www.ccdc.cam.ac.uk). However,for many users, this resource is not available on-line.
Mac Os X Download 10.6
A list of sites that hold small molecule co-ordinates (and additional proteinstructures) is Eric Martz'z 'Molecules Galore!' WWW page athttp://www.umass.edu/microbio/rasmol/whereget.htm
[This answer was derived in part from the RS response to this question. -- HJB]
Why won't RasMol 2.7 display my bond orders?
Older versions of RasMol infer bond orders from redundantCONECT records for some molecules in a psuedo-PDB format.Unfortunately, this would cause the display of incorrectbond orders for some valid PDB format files which hadredundant CONECT records for other reasons. The featurehas been disabled until a consistent and reliablealternative can be found.
How do I measure distances within RasMol?
There are two ways to measure distances between atoms in ...RasMol. The first is to use the 'set picking distance' command, to set the mouse into interactive distance measurement mode. Then by clicking on pairs of atoms, RasMol will report the distance between them on the command line. RasMol also has similar modes for 'set picking angles' and 'set pickingtorsions'. The mouse can be returned to the default mode using 'set picking ident'.The second approach is to use distance monitors. A distance monitorin RasMol is a graphical dotted line between an arbitrary pair of atomsoptionally labelled by the distance between them. There are two waysto add a monitor to a molecule. The first is to use 'set pickingmonitors', similar to set picking distance above. Note that this willacta as a toggle and selecting the same two atoms again will remove themonitor. Monitors can also be added from the command line using themonitor command. This command takes the atom serial numbers of thetwo end-point atoms as parameters. All monitors can be turned of usingthe command 'monitors off'.
--RS
How do I select residues in a particular chain?
The method for selecting a range of residues in a particular chain ... improved in RasMol version 2.6. It can now be done using the syntax 'select 1-25:a' to select residues 1 to 25 in chain A. Similarly 'select 25:a' and 'select :a' will select just residue 25 in chain A and all of chain A, respectively.In RasMol versions prior to v2.6, you'd have to type an atom expression of the form 'select 1-25 and **a' where the final term is a primitive expression. This primitive expression is a wildcarded formof the form 'cys37a' where the residue name and number are replaced by the wildcard '*'.
Note that care has to be made to ensure that RasMol can determine which field is being specified. For example, although 'select *a' will select all residues in chain A, if the chain identifier was a number, 'select **1' would have to be used, as 'select *1' denotesresidue 1. To avoid any ambiguity, an optional colon character is now used to prefix the chain identifier, allowing expressions such as'cys:a', 'cys35:1', '*:1' and even just ':1'.
See also the RasMol Manual.
--RS
How can I create the PDB file for a particular sequence?
May I strongly recommend that you consider using the Swiss-Modelserver, written by Manuel Peitsch at the University of Geneva. Thise-mail and WWW server accepts as input either an amino-acid sequenceor a multiple sequence alignment with a protein of known structureand performs comparative homology modelling to return the potential3D structure to you by e-mail as a PDB file.For more information visit the Swiss-Model WWW page at www.expasy.ch/swissmod/SWISS-MODEL.html
--RSI can't find the command line window in RasWin
This is a confusing problem with RasWin. When RasWin startsunder Microsoft Windows the command line window is initially iconised(unlike the Macintosh or UNIX versions). The 'RasMol Command Line'icon appears at the bottom of the screen on the Windows background.Unfortunately, this is often obscured by another window such as theProgram Manager or the File Manager. Both the 'RasMol' icon and the'RasMol Command Line' icons can be seen if all the open windows are minimized.A more convenient solution is to make use of the Microsoft 'Alt-Tab'control key combination. Hold down the 'Alt'-key, and press the 'Tab' key one or more times until the name of the window you wish to bringto the front appears, then release the 'Alt'-key.
--RSHow do I create high resolution images in RasMol?
Unfortunately, raster images generated by RasMol are currently limited by the screen resolution (though this deficiency is actively being worked on).This means that images will generated at the resolution of about 72dpi(dots per inch) even though most printers (including colour printers) support resolutions of 300dpi, 450dpi or even 600dpi. This leads tojagged bitmap like printouts where the individual pixels are often visible.The exception to the above rule is images produced in Vector Postscriptformat using the 'write vectps' command. These output files have the advanatge of being generated at the printer's resolution, but the disadvantage of not supporting all of RasMol's representations.
One way to minimise the limitations of screen resolution is to expand ormaximise the RasMol graphics window to the full size of the screen before generating an output file. This ensures that the image contains as muchdetail as possible. Another commonly used trick is post-process the imagein a graphics package such as PhotoShop or 'xv' to expand and then bluror smooth the images generated by RasMol.
...
As mentioned above RasMol's resolution limitations are currently beingremoved by four approaches:
- Support for high resolution output images (at x4 screen resolution).
- The ability to have large resolutions in UNIX command-line only mode.
- Vector PostScript support for all RasMol representations.
- Export of model file formats (including POV, Raster3D, DXF and VRML) to other rendering programs such as photo-realistic ray-tracers.
Generating RasMol animations non-interactively in UNIX
The inability to use theRasmol Program
save and write commandsin a RasMol script file is a deliberate security feature.There was a concern about the security of using RasMol on the Internet when researchers started e-mailing and FTPing 'untrusted' script files between sites. This was especially true of sites that have configured Netscape to fire up RasMol with a RasMol script file MIME type.Such a script, executed with 'rasmol -script <filename>' may potentially overwrite system and user files, for example creating a '~/.rhosts' file on the remote machine. To defend against this threat I decided to disable the save and write command from within RasMol, unless the command 'set write true'had been entered interactively on the command line.The solution to the problem is to run your scripts with:ori.e. pipe the commands into stdin. RasMol can't tell that these haven'tbeen generated interactively and allows save and write commands.
--RSIs there an Acorn Archimedes version of RasMol?
The Acorn Archimedes (ARM) version of RasMol has been ported by MartinWuerthner at the University of Stuttgart,'wuerthne@trick.informatik.uni-stuttgart.de'. The Archimedes distribution is available at the following sites:HENSA (difficult to reach for users from outside the UK):micros.hensa.ac.uk (in /micros/arch/riscos/e/e089/rasmol.arc),the University of Kaiserlautern (Germany):ftp.uni-kl.de (in /pub/acorn/long/science/chemistry/rasmol.arc),and the University of Stuttgart (Germany):ftp.uni-stuttgart.de (in /pub/systems/acorn/riscos/etc/rasmol110.spk).
The first RISC OS release (1.10) of RasMol has the following features inaddition to those of the X version:
- runs on all Acorn 32-bit RISC computers under RISC OS 3.1 or higher, supports all display depths up to 24 bpp, just about runs on a 2MB machine
- fully supports RISC OS cooperative multitasking even while rendering the image
- Floyd-Steinberg colour dithering for 16 and 256 colour modes
- support of both the RasMol mouse mode and a more RISC OS-like way using a tool bar with rotation/translation/slabbing etc. tools
- extended menu structure (e.g. sub-menus to enter parameters for display options)
- exports native RISC OS bitmap format, RISC OS drag-and-drop support
--RS
The latest release for the Acorn is the RISC OS port of RasMol 2.7.1 (RISC OS port version 1.31b) (see http://www.mw-software.com/software/rasmol/rasmol.html).
Is there an MacOS X version of RasMol?
The short answer is yes -- see the sourceforge openrasmol site.
Why can't I see my data files in Classic under Mac OS X?
If you create data files under Mac OS X in order to load them intothe Classic version of RasMol, you may need to set the 'creator'and 'file type' of the files to make then visible to Classic.Apple provides a utility, SetFile, in the Developer Tools that will do the job.First you need to install the Developer Tools from CD or from the Appleweb site developer.apple.com/tools/download/. You should then be able to find SetFile at /Developer/Tools/SetFile. Usinga terminal window, change your directory to the one containing the file youcannot see and execute
/Developer/Tools/SetFile -t 'TEXT' filename
where filename is the name of the file you need to see as a PDBdata file in a Classic version of RasMol
--HJB
How do I see RasMol's stereo pairs in 3D?
See Gale Rhodes' excellent guide to viewing stereo image pairs,Stereo Viewing.--EM
What is the relationship among the various RasMol web sites?
There is no connection between the molecular graphics program RasMol andthe rasmol.com web site. The www.RasMol.org, www.OpenRasMol.org and www.OpenRasMol.com sites are all the same site, the home page for the molecular graphic program RasMol.Eric Martz's site www.umass.edu/microbio/rasmol/is focused on Protein Explorer and Chime. Even though it is badly outof date with respect to RasMol, it contains a great deal of usefulinformation, and maintains a discussion list for those interested inRasMol.
We have notified that holders of rasmol.com that they are causing confusion with our marks by using the name rasmol for their site, butthey have not, to date (15 June 2002), responded to our email. One might speculate that they are using the popularity of the name to draw 'eyeballs' for the advertising on their site. Please note thatthe RasMol project does not draw any revenue or other benefitfrom such advertising. -- HJB
| RasMol Manual |Frequently Asked Questions |RasMol 2.7 Series History |RasMol and OpenRasMol |
| Click Here to Make a Donation |
www.OpenRasMol.org/FAQ.html
Biomolecular Structures Group, Glaxo Wellcome Research & Development
Stevenage, Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright © Roger Sayle 1992-1999
| Author | Version, Date | Copyright |
|---|---|---|
| Arne Mueller | RasMol 2.6x1 May 1998 | © Arne Mueller 1998 |
| Gary Grossman and Marco Molinaro | RasMol 2.5-ucb November 1995 RasMol 2.6-ucb November 1996 | © UC Regents/ModularCHEM Consortium 1995, 1996 |
| Philippe Valadon | RasTop 1.3 August 2000 | © Philippe Valadon 2000 |
| Herbert J. Bernstein | RasMol 2.7.0 March 1999 RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001 RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001 RasMol 2.7.2.1.1 January 2004 | © Herbert J. Bernstein 1998-2004 |
| Author | Item | Language |
|---|---|---|
| Isabel Serván Martínez, José Miguel Fernández Fernández | 2.6 Manual | Spanish |
| José Miguel Fernández Fernández | 2.7.1 Manual | Spanish |
| Fernando Gabriel Ranea | 2.7.1 menus and messages | Spanish |
| Jean-Pierre Demailly | 2.7.1 menus and messages | French |
| Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto | 2.7.1 menus and messages 2.7.1 help file | Italian |
Herbert J. Bernstein,Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright © Herbert J. Bernstein 1998-2001
The original RasMol manual was created by Roger Sayle. In July 1996,Dr. Margaret Wong of the Chemistry Department, Swinburne Universityof Technology, Australia, made extensive revisions to the RasMol 2.5manual to accurately reflect the operation of RasMol 2.6. Eric Martzof the University of Massachusetts made further revisions. In May1997, William McClure of Carnegie Mellon University reorganized theHTML version of the manual into multiple sections which could bedownloaded quickly and added use of frames. Portions of the 2.7.1version of the RasMol manual were derived with permission fromWilliam McClure's version using Roger Sayle's rasmol.doc forversion 2.6.4 as the primary source. Changes were made inAugust 2000 for RasMol version 2.7.2, January 2001 for RasMolversion 2.7.1.1 and April 2001 for RasMol version 2.7.2.1.
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel FernándezFernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada.España (jmfernan@ugr.es)) a translation of theManual for Rasmol version 2.7.1 into Spanish is now available.La traducción española del manual de laversión de la Dra. Wong revisada por Eric Martz fue realizada porIsabel Serván Martínez y José Miguel FernándezFernández. La actual traducción del Manual de RasMol 2.7.1ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea
Production Release
RasMol 2.7.2.1.1 is the production release of version 2.7.2 of the RasMol 2.7series. Aside from code cleanups to avoid compiler warning messages, andone bug fix (to allow reading of the RCSB PDB mmCIF extensions data sets),this release is the same as the April 2001 2.7.1.1 release.
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.2, on RasMol 2.7.1.1,on RasTop 1.3, on RasMol version 2.6_CIF.2, on RasMol version2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb.Please read the file NOTICE forimportant notices which apply to this package. If you are not going tomake changes to RasMol, you are not only permitted to freely make copiesand distribute them, you are encouraged to do so, provided you do thefollowing:
- 1. Either include the complete documentation, especially the file NOTICE, with what you distribute orprovide a clear indication where people can get a copy of the documentation; and
- 2. Please give credit where credit is due citing the version andoriginal authors properly; and
- 3. Please do not give anyone the impression that the original authorsare providing a warranty of any kind.
If you would like to use major pieces of RasMol in some other program, makemodifications to RasMol, or in some other way make what a lawyer would calla 'derived work', you are not only permitted to do so, you are encouragedto do so. In addition to the things we discussed above, please do thefollowing:
- 4. Please explain in your documentation how what you did differs fromthis version of RasMol; and
- 5. Please make your modified source code available.
This version of RasMol is not in the public domain, but it is givenfreely to the community in the hopes of advancing science. If you makechanges, please make them in a responsible manner, and please offerus the opportunity to include those changes in future versions of RasMol.
This file explains how to transfer, compile and install RasMol v2.7.2.1.1on your system. This version of the RasMol Molecular graphics package will run on UNIX, VMS, Macintosh and Microsoft Windows.
Obtaining RasMol v2.7.2.1.1
This version of RasMol may be obtained by anonymous FTP either byanonymous FTP at:
ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1
or on the web at:
To transfer by anonymous ftp, type 'ftp ftp.bernstein-plus-sons.com' on the commandline. Several seconds later you'll be prompted for a username. Use theusername 'anonymous' and when asked for a password enter your e-mailaddress. Once logged in, type the command 'cd software/rasmol' to changethe directory to /software/rasmol and then type 'binary' to avoid corruptingthe files during the transfer. For each file you wish to transfer, type'get <filename>' and when you've finished type 'quit'. If these files are subsequently transfered to other machines, please remember totransfer them in BINARY mode. The file sizes should be identical beforeand after the transfer.
NOTE: The Mac uses the 'carriage return' character to signify theend of a line, while UNIX machines use a 'linefeed'. If a file istransfered between these two machines in 'ASCII' mode all suchcharacters are exchanged, thereby corrupting the archive. Pleaseensure that you type the FTP command 'binary' before you transfer thefile, indicating that the file should be transfered withouttranslation.
To build/rebuild RasMol 2.7.2.1.1 on any platform, you'll need to transfer the following file:
| RasMol.tar.gz | UNIX 'tar'ed 'gzip'ped archive containing the complete source code and documentation of the RasMol molecular graphics package. |
To unpack the file on a UNIX machine type the command 'gunzipRasMol.tar.gz' and then the command 'tar -xvfRasMol.tar' to extract the files in a subdirectory under thecurrent directory.
There are command-line and GUI-interface versions of tar and gzip forthe Macintosh and for Windows, so we have discontinued the formerpractice of providing StuffIt or ZIP archives for those platforms.However, note that MacIntosh-specific files are actually provided in gzippedMacBinary form with a '.bin.gz' extension.
Important Note for Mac OS X: If you simply unpack the tarunder Mac OS X, but use an application to compile, such a CW 5.3,to compile under Mac Classic, you will need to set the creatorand type using SetFile in the Apple Developer Tools. You willalso need to make similar settings for the sample data filesin the data directory. The scripts src/CW_fixup.cshand data/RSML_fixup.csh are providedto assist in this fixup after you have installed theApple Developer Tools.
If you are in a hurry, the following pre-compiled binary files are available:WARNING: ALL binaries and help files are gzipped!!! Uncompressedbinaries are also available in the second section of each page.
| DEC/Compaq/HP: | RasMol.DEC |
|---|---|
| HP: | RasMol.HP |
| Linux (RedHat 7, i386): | RasMol.LINUX |
| Mac: | RasMol.MAC |
| MS Windows: | RasMol.MSWIN |
| RS/6000: | RasMol.RS6K |
| SGI: | RasMol.SGI |
You will need both an appropriate binary and a copy of rasmol.hlp for eachsystem, and, under Windows, a copy of raswin.hlp for the WinHelp sub-system.
On an SGI, rename the appropriate binary as rasmol and copy it to/usr/local/bin/rasmol (or to some appropriate location specifiedby the environment variable PATH) and copy rasmol.hlp to/usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by theenvironment variable RASMOLPATH)
Installing RasMol v2.7.2.1.1
UNIX X11:
- In the src subdirectory: Type the command 'xmkmf' to generate a 'Makefile' for your particular system from the distributed Imakefile Alternatively (or if the first method fails), copy the file Makefile.in to Makefile, using the command 'cp Makefile.in Makefile', then modify the contents of the Makefile to determine your local C compiler, compiler and linker options. The default set up is for an 8bit UNIX workstation with the X11 shared memory extension, compiled using the GNU C Compiler. Changing the line 'CC=gcc' to 'CC=cc' will use the machines native compiler but will require changing 'CFLAGS' for your platform. A common problem is that SUN OpenWindows keeps its include files in the directory /usr/openwin/include/X11, hence the compiler directive -I/usr/openwin/include must be added to CFLAGS. A common problem on IBM RS6000s running AIX is that the MIT shared memory extensions to X windows are in the library -lXextSam, hence this must be added to the LIBS lines in either the Makefile or Imakefile.
- Modify the #defines in the file rasmol.h (see below) Note: IBMPC should not be defined.
- Compile the program using the UNIX make utility. (i.e. type 'make')
- Place the 'rasmol' executable on the execution PATH, i.e. /usr/local/bin
- Install rasmol.hlp as /usr/local/lib/rasmol/rasmol.hlp (or at a loctaion indicated by the environment variable RASMOLPATH).
- If you have the UNIX utilities 'uncompress' or 'gunzip' ensure they are on the user's default PATH.
- Set the environment variable RASMOLPDBPATH to the directory containing the Broohaven PDB database, if one exits.
- Place any system wide initialisation parameters into the file 'rasmolrc' in the directory pointed to by RASMOLPATH.
- It is possible to set-up RASMOLPATH and RASMOLPDBPATH each time the program is running by renaming rasmol to rasmol.exe, and using a script similar to the one in 'rasmol.sh' of the standard distribution.
- If appropriate place 'rasmol.1' or 'rasmol.0' in the appropriate place for UNIX man pages, and optionally place 'rasmol.html' somewhere in your WWW hierarchy (if available at your site).
MS Windows:
- Copy the executable RASWIN.EXE and the help files RASMOL.HLP and RASWIN.HLP to an appropriate directory. You may execute the program immediately by double-clicking the icon of RASWIN.EXE.
- Under Windows/95 and similar systems, create a shortcut icon to RasWin on the Desktop or in a folder. Select the RasWin icon then simultaneously press ALT-ENTER (or right click on the icon and select 'Properties' from the menu). Select the 'Shortcut' tab in the Properties dialog box.
- At the 'Start In:' prompt, type in the path of the appropriate working directory.
- Under Windows 3.1 and similar systems Install the program in MS Windows using the New option of the Program Manager's File Menu. Set the Description of the Program to 'RasWin v2.7.2.1.1' and the Current Directory, to the directory containing the files. Install the RasMol Help file using the New option of the Program Manager's File Menu. Set the Description to 'RasWin Manual', the command to 'C:WINDOWSWINHELP RASWIN.HLP' and the working directory to the appropriate directory.
Macintosh and PowerMac:
- Place both 'RasMac_FAT' (or 'RasMac_PPC' or'RasMac_68k)' and 'rasmol.hlp' in the same Macintosh folder
VAX/VMS:
- There is a VMS-ready copy of rasmol.h in the 'src/vms' directory. Modify the #defines in the file rasmol.h (see below) Note: IBMPC, MITSHM and TERMIOS should not be defined.
- Copy all the files from the 'src/vms' directory to the source directory.
- Copy the file 'rasmol.hlp' from the 'doc' directory to the source directory.
- If your VAX site has an MMS license type the command 'MMS', otherwise use the DCL build script by typing '@build.com'
- The program may be run by typing 'RUN RASMOL.EXE', the X Windows server is specified by a VMS command of the form:
SET DISPLAY/CREATE/TRANSPORT=TCPIP/NODE=<hostname> - The symbol RASMOL should be defined to be the path of RASMOL.EXE using :
- The file doc/rasmol.vms contains a ascii VMS help file that can be compiled in to the VMS on-line help system.
Recompiling RasMol v2.7.2.1.1
For both Windows and Mac, this version has been built with MetroWerksCodeWarrior, and the necessary projects are included in the src/mswin andsrc/mac directories. The following more general instructions adapted from theRasMol v2.6 release are provided for your information, but have _not_ beentested against RasMol_2.7.2.1.1:
MS Windows v3.1:
- Use Makefile.pc instead of Makefile, by copying it to MAKEFILE.
- Modify the contents of the Makefile to determine your local C compiler, compiler and linker options.
- Modify the #defines in the file rasmol.h (see below) Note: EIGHTBIT and IBMPC should all be defined APPLEMAC, DIALBOX, MITSHM and TERMIOS should not be defined.
- Compile the program using the Microsoft Optimizing C Compiler Version 7's (or Microsoft Visual C++'s) NMAKE program under MS-DOS.
MS Windows
- Using Microsoft Visual C++, create a new project adding all the '*.c' source files except 'rasmol.c', 'x11win.c', 'rasmac.c' and 'applemac.c'. Add the Windows resource source file 'raswin.rc'. or alternatively use Makefile.nt by copying it to MAKEFILE.
- Follow the instructions from [2] onwards as for MS Windows v3.1.
Apple Macintosh and PowerMac
- Create a project in either the Symmantec C/C++, Think C or Metrowerks C compiler environments and add all the C source files ('*.c') to the project. On 68k development systems all C files should be placed in separate segments [however rasmac.c and applemac.c can share a segment and abstree.c and command.c can share a segment].
- Add the 'rasmac.rsrc' resource file to the project.
- For the Symantec/Think C environment add the 'ANSI' or 'ANSI-small' library from 'Standard Libraries' folder and the 'MacTraps' library from the 'Mac Libraries' folder. The choice of 'ANSI' or 'ANSI-small' is dependent upon the size of integer by the compiler. See dialog 'Edit'->'Options'->'Think C..'->'Compiler Settings'. 2-byte integers require 'ANSI-small' and 4-byte integers require 'ANSI'.
- A project files has been provided for Metrowerks 68K, PPC and FAT versions.
- If that project file is not satisfactory, for the Metrowerks 68K Compiler add the libraries 'MacOS.lib' and 'ANSI (2i) C.68K.Lib' to the project. [Note: If compiling for 4byte integer size and/or 68881 maths instructions select the approriate ANSI C Library].
- For some Metrowerks 68K compiler releases the 'C/C++ Language Settings' 'Enums Always Int' must be selected for proper execution.
- For the Metrowerks PPC Compiler add the libraries 'MWCRuntime.Lib', 'InterfaceLib', 'MathLib' and 'ANSI C.PPC.Lib'. This should work fine for Metrowerks C++ v1.1. Apparently, Metrowerks C++ v1.2 also requires 'console.stubs.c'. [Thanks to Graham Palmer]
- In Metrowerk's 'Edit' 'Preferences' 'Project' or Symmantec's 'Project' 'Set Project Type', set the project type to Application (Type 'APPL'), Creator 'RSML', and the SIZE flags to include 'is32bitCompatible', 'isHighLevelEventAware', 'localAndRemoteHLEvents'.
- Modify the #defines in the file 'rasmol.h' (see below). Note: APPLEMAC should all be defined IBMPC, DIALBOX, MITSHM and TERMIOS should not be defined.
- Compile RasMol using the 'Build Application...' Menu Item.
- To create a `fat' binary, use Apple's ResEdit to copy and paste the CODE, DATA and XREF resources from the Metrowerks 68K executable into the resource fork of the Metrowerks PPC executable.
- The Installed Application's name should be 'RasMac v2.7.2.1.1'
COMPILATION DIRECTIVES
The file rasmol.h contains a number of #define directives that controlthe runtime behaviour of the program. The following directives may bedefined or undefined to suite the local site.
| THIRTYTWOBIT SIXTEENBIT EIGHTBIT | This determines whether RasMol will display and produce 8bit, 16bit or 32(24) bit output. By default the symbol EIGHTBIT is defined producing images with up to 256 colours. This symbol must be defined if IBMPC is defined. |
| DIALBOX | This enables the use of a dials box, that is connected using the X Window System XInput extension. This option requires that the program be compiled with the Xi and Xext libraries. Note: libXi is called libXinput on some old machines, so requires the compiler option -lXinput! |
| MITSHM | This option enables the use of the X Window System MIT shared memory extension. This enables images to be displayed faster when RasMol and the X11 server are running on the same host. This option requires the program be compiled with the Xext library. On IBM RS6000s runnning AIX, MITSHM also requires the XextSam library (which requires changing the Makefile or Imakefile). This is now enabled by default. This should be disabled on E&S ESV workstations as MITSHM support is not provided as standard. |
| TERMIOS | This directive enables the command line processing on UNIXs that support the termios terminal handling routines. By leaving this symbol undefined, RasMol omits the interactive command line interface. Undefining is not recommended! |
| SOCKETS | This directive enables the TCP/IP server functionality of RasMol to be enable. This enables other software to connect to a running RasMol. This should be undefined on machines not supporting BSD-style TCP/IP sockets (such as VMS). |
| APPLEMAC | This determines whether the program is to run on an Apple Macintosh or PowerMac. By default, this option is disabled. The Macintosh code may be compiled to be either EIGHTTBIT or THIRTYTWOBIT and will generate images effectively. |
| IBMPC | This determines whether the program is intended to run on an IBM PC or compatible. By default, this option is disabled. |
| MSWIN | This determines whether the program is intended to run on an IBM PC or compatible under MS Windows. By default, this option is disabled. |
| PROFILE | Defining PROFILE enables code to profile RasMol execution. |
To summarise;
Any comments, suggestions or questions about thismodified version should be directed to Herbert J. Bernstein atrasmol@bernstein-plus-sons.com.
| Changes |Things To Do |Introduction | Source Code and Binaries |
| RasMol Manual |Spanish Translation of RasMol Manual | Italian Translation of RasMol Help File |
| Release README |
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com