RasMol Frequently Asked Questions

Roger Sayle, Glaxo Wellcome Research and Development

Can RasMol be distributed freely, on CD-ROMs, and used freely even for commercial purposes?

Here is a quote from Roger Sayle, author of RasMol, in reply to a 1998 inquiry about commercial use of RasMol:
The RasMol molecular graphics package is "public domain", which in the legal definition is more than just freely redistributable but actually free of all intellectual property right. Although my original vision was to allow it to be redistributed at the back of text books and enable researchers like Eric to collaborate in its development. Indeed about 8 publishers currently bundle it with CD-ROMs or text books, and several people actively continue to independently develop and support RasMol. However the darker side of "public domain" is that companies such as MDL and MSI are able to sell it as a stand-alone product for profit, not only without roytalty but in some cases without acknowledgement. Hence I'm delighted for you to bundle it with your text's and theres nothing to stop you selling it for profit. But then if another publisher also sells the same stand-alone cheaper, or a customer wishes to download it from the internet for free, there's nothing you can do to prevent them. I hope this explains the situtation. Please have my blessing to use it as you will, in the end it is the research community that stands to benfit most.
Roger Sayle, E-mail: roger@metaphorics.com 
Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 
419 East Palace Avenue, Tel: (+1) 505-984-0613 
Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200

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.

What is the definitive literature citation 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.

Where can I get more molecule co-ordinate files?

In addition to the three example files that are distributed with RasMol, the protein crambin (1crn.pdb), the DNA-binding protein CRO (3cro.pdb) and aspirin (asprin.alc), the major source of data files for RasMol is the Protein Databank at Brookhaven National Labs. 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 over 7,000 are available at the Protein Data Bank. One of the best lists 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

How do I measure distances within RasMol?

There are two ways to measure distances between atoms in version 2.6beta of 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".

How do I select residues in a particular chain?

The method for selecting a range of residues in a particular chain has 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 resiues 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.

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 Manual Peitche 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

I can't find the command line window in RasWin

This is a confusing problem with RasWin. When RasWin initially 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.

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.

How do I create high resolution images in RasMol?

Unfortunately, raster images generated by RasMol are currently limited by the screen resolution (though this defficiency is actively being worked on). This means that images will generated at the resolution of about 72dpi (dots per inch) even though must 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.

See also the discussion on this topic in the RasMol FAQ by Martz.

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.

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>
        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.

Is there an Acorn Archimedes version of RasMol?

Note: all known versions of RasMol for different operating systems, including Acorn RISC, are available through the Getting RasMol page.

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:

1996 Roger Sayle