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
Roger Sayle, E-mail: email@example.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
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
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
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
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
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
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
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
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:
- 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 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
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,
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:
- 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
- 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
- exports native RISC OS bitmap format, RISC OS drag-and-drop support
1996 Roger Sayle firstname.lastname@example.org