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Frequently Asked Questions (FAQ)
for
OpenRasMol

RasMol
 
Molecular Graphics Visualisation Tool

RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users and software developers of open source versions of RasMol. In order to ensure continuing availability of source code and documentation most programs and documents on this site are subject to copyright. This does not prevent you from using the open-source versions of RasMol, from making copies and changes, but prevents the creation of "closed source" versions out of the open source versions. Appropriate copyrights and licenses appear with the relevant sources and documents. See Copyright and NOTICE for 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 at http://www.umass.edu/microbio/rasmol/faq.htm, one FAQ by Roger Sayle, and one by Eric Martz. The portions of the FAQs from the Martz web site are included by permission of Eric Martz. Many of the questions in this document are the same or similar to those in the earlier FAQs, but some of 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 University of Technology, Australia, made extensive revisions to the RasMol 2.5 manual to accurately reflect the operation of RasMol 2.6. Eric Martz of the University of Massachusetts made further revisions. In May 1997, William McClure of Carnegie Mellon University reorganized the HTML version of the manual into multiple sections which could be downloaded quickly and added use of frames. Portions of the 2.7.1 version of the RasMol manual were derived with permission from William McClure's version using Roger Sayle's rasmol.doc for ˆversion 2.6.4 as the primary source. Changes have been made in August 2000 for RasMol version 2.7.2.

The RasMol documentation was adapted for RasTop by Philippe Valadon in August 2000.

RasTop Documentation Last Updated 15 September 2000
Edited by Philippe Valadon

Documentation Last Updated 15 September 2000
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 might interest 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 files as if they were ordinary text files. They are all binary files. In some cases, a browser can be convinced to do a binary download by holding down one of the shift keys (Alt, Opt, Shift, etc.), while clicking on the download link. If that does not work, then you will have to download gzipped files and unpack them under Windows. Sometimes your browser will be willing to download the gzipped files as binary files, but if that does not work, you will have to resort to the File Tranfer Protocol (FTP) client packaged with all copies of Windows.


I get the message "No suitable display detected!"

This is a problem on the UNIX version of RasMol caused by one of two potential problems. The first is that your DISPLAY environment variable isn't set corrrectly or that you don't have permission to display to the X Windows server. This can be checked 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 been compiled in 24/32bit mode (by defining THIRTYTWOBIT in either rasmol.h or Makefile). The 24/32bit mode indicates that RasMol should use 3bytes/pixel (or 16 million simultaneous colours). If the current X Windows server is unable to display this visual depth it reports the "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 with EIGHTBIT defined instead (i.e use one byte/pixel or 256 simultaneous colours).

Note: that RasMol must be configured with EIGHTBIT for 1bit/pixel (monochrome) or 8bit/pixel displays, with SIXTEENBIT for 16bit/pixel displays and with THIRTYTWOBIT for either 24bit/pixel or 32bit/pixel displays.

--RS

In pactice on most UNIX systems, the fastest way to change the pixel bit depth after a 'xmkmf' has been done, is to edit the file 'Makefile', commenting out the wrong definition (i.e. of EIGHTBIT, SIXTEENBIT or THIRTYTWOBIT) and uncommenting the right definition. Then 'make clean' followed by 'make' should correct 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 we have 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, and used freely even for commercial purposes?

Different versions of RasMol have had different rules for redistribution. The rules for the RasMol 2.7 series are intended to allow redistribution on an "open source" basis. The idea is to encourage distribution of RasMol and programs derived from RasMol provided source code and documentation remain available, and a few other sensible conditions are accepted by the distributor.

Starting with RasMol release 2.7.3, RasMol may be distributed under the GPL, one of the most popular open 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 program based on RasMol?

If what you mean by "commercial" is that you want to distribute binary 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 wish to sell programs and services based on RasMol, that you certainly may do. Just remember that your new and wonderful program has to include or reference all the original source code and documentation, including the file NOTICE, which will allow other people to copy your program. In other words the rules for distributing copies of RasMol that you have taken advantage of will also apply to people who wish to make copes of your program.

A lot of people find it easy to work within this framework, but if you need to do commerical development which does not fit the open source model, you may not make use of any substantial portion of the RasMol 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 binaries of the 2.7 series to run under Linux. Starting with the RasMol 2.7.3 release, RasMol may be distributed under the GPL. However, earlier RasMol 2.7 releases are not covered by the GPL. Those RasMol 2.7 releases have their own "GPL-like" license (RASLIC, which carefully avoids certain issues which, until recently, would have caused problems if we had used the GPL for those releases. Those problems have now 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 single caveat. RasMol can read and write MDL Mol and Brookhaven PDB files, which reserve only two characters for the year in a date field. RasMol ignores these fields and is therefore not affected by Y2K. However programs reading MDL Mol files generated by RasMol (or any other molecular graphics program) may suffer if they process the date field.
--RS

In addition, please note that we are now well past 31 December 1999, and there 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 that all 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 use the Latin-1 (ANSI), Macintosh, or MS Windows OEM characters sets, without explicit support for the Euro symbol, which might cause RasMol to be rejected in testing for "Euro compliance" against standards intended 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 is the Protein Data Bank operated by the Research Collaboratory for Bioinformatics (see http://www.rcsb.org/pdb). This is the main repository for all of the world's known 3D xray-crystallography and nuclear magnetic resonance (NMR) structures of proteins and nucleic acids. Currently (September 2000) over 13,000 are available from mirror sites throughout the world (see http://www.rcsb.org/pdb/mirrors.html

The primary archive for three dimensional structures of small molecules is the Cambridge Crystallographic Data Centre, with over 200,000 organic and metal organic compounds (see http://www.ccdc.cam.ac.uk). However, for many users, this resource is not available on-line.

A list of sites that hold small molecule co-ordinates (and additional protein structures) is Eric Martz'z "Molecules Galore!" WWW page at http://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 redundant CONECT records for some molecules in a psuedo-PDB format. Unfortunately, this would cause the display of incorrect bond orders for some valid PDB format files which had redundant CONECT records for other reasons. The feature has been disabled until a consistent and reliable alternative 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 picking torsions". The mouse can be returned to the default mode using "set picking ident".

The second approach is to use distance monitors. A distance monitor in RasMol is a graphical dotted line between an arbitrary pair of atoms optionally labelled by the distance between them. There are two ways to add a monitor to a molecule. The first is to use "set picking monitors", similar to set picking distance above. Note that this will acta as a toggle and selecting the same two atoms again will remove the monitor. Monitors can also be added from the command line using the monitor command. This command takes the atom serial numbers of the two end-point atoms as parameters. All monitors can be turned of using the 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 form of 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" denotes residue 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-Model server, written by Manuel Peitsch at the University of Geneva. This e-mail and WWW server accepts as input either an amino-acid sequence or a multiple sequence alignment with a protein of known structure and performs comparative homology modelling to return the potential 3D 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

--RS

I can't find the command line window in RasWin

This is a confusing problem with RasWin. When RasWin starts under 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 the Program 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 bring to the front appears, then release the "Alt"-key.

--RS

How 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 to jagged bitmap like printouts where the individual pixels are often visible.

The exception to the above rule is images produced in Vector Postscript format 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 or maximise the RasMol graphics window to the full size of the screen before generating an output file. This ensures that the image contains as much detail as possible. Another commonly used trick is post-process the image in a graphics package such as PhotoShop or "xv" to expand and then blur or smooth the images generated by RasMol.

...

As mentioned above RasMol's resolution limitations are currently being removed by four approaches:

  1. Support for high resolution output images (at x4 screen resolution).
  2. The ability to have large resolutions in UNIX command-line only mode.
  3. Vector PostScript support for all RasMol representations.
  4. Export of model file formats (including POV, Raster3D, DXF and VRML) to other rendering programs such as photo-realistic ray-tracers.

--RS

Generating RasMol animations non-interactively in UNIX

The inability to use the save and write commands in 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:

        rasmol -nodisplay <pdbfile> < <scriptfile>
or
        cat <scriptfile> | rasmol -nodisplay <pdbfile>
i.e. pipe the commands into stdin. RasMol can't tell that these haven't been generated interactively and allows save and write commands.

--RS

Is there an Acorn Archimedes version of RasMol?

The Acorn Archimedes (ARM) version of RasMol has been ported by Martin Wuerthner 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 in addition to those of the X version:

--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 Accessible Retired Computers in Biology (ARCiB) website.

The long answer is as follows. MacOS X has three different ways to run a graphics program: as a native Aqua interface program, as an XDarwin X-Windows program (see www.XDarwin.org and www.XFree86.org), or as a Mac Classic program. You can run the existing Mac versions of RasMol as Mac Classic programs using drag and drop file opening, but there is a problem with the menu-driven file-open dialog. Fortunately, the RasMol source code builds correctly using Apple's MacOs X Developer's Tools, and runs under XDarwin 4.2. Thanks to the efforts of various interested users, there have been versions of RasMol adapted to MacOS X in this way for some time. Unfortunately, many of the links posted seem to be broken, or lead you to builds based on older versions of RasMol. Therefore we have done a clean build of RasMol 2.7.2.1 on MacOS 10.2.2 (Darwin 6.2) using XDarwin 4.2.1.1 and posted the binaries on the Accessible Retired Computers in Biology web site. There are 8-, 16- and 32-bit versions. We recommend the32-bit version. In order to use these binaries, you need to do the following:

RasMol should now start whenever XDarwin is started by

startx -- -quartz or startx -- -rootless If you would like a cleaner way to run RasMol under XDarwin that gives you an Aqua style X-windows interface, download OroborOSX from oroborosx.sourceforge.net.


  • 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 into the 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 Apple web site developer.apple.com/tools/download/. You should then be able to find SetFile at /Developer/Tools/SetFile. Using a terminal window, change your directory to the one containing the file you cannot see and execute

    /Developer/Tools/SetFile -c "RSML" filename
    /Developer/Tools/SetFile -t "TEXT" filename

    where filename is the name of the file you need to see as a PDB data 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 and the 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 out of date with respect to RasMol, it contains a great deal of useful information, and maintains a discussion list for those interested in RasMol.

    We have notified that holders of rasmol.com that they are causing confusion with our marks by using the name rasmol for their site, but they 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 that the RasMol project does not draw any revenue or other benefit from such advertising. -- HJB


    | Copying and Distribution | Contents | Software Distributions |
    | RasMol Manual | Frequently Asked Questions | RasMol 2.7 Series History | RasMol and OpenRasMol |
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    www.OpenRasMol.org/FAQ.html


    The OpenRasMol site is provided courtesy of Bernstein + Sons, Information Systems Consultants.
    Portions © Copyright Herbert J. Bernstein 2000, 2006. All Rights Reserved. Other copyrights apply. License to copy most pages on this site will be granted if certain open source and other conditions are adhered to. See http://www.OpenRasMol.org/Copyright.html. To request permission to copy any elements from our pages, or to send comments about our pages, please write to webmaster@OpenRasMol.org. If you establish a link to one of our pages, please let us know! Updated 29 April 2005