Molecular Graphics Visualisation tool.
BioMolecular Structures Group
Glaxo Research & Development
Greenford, Middlesex, UK.
This posting is to announce the release of RasMol version 2.5. This
latest version is available for the Apple Machintosh and PowerMac in
addition to UNIX, VMS and Microsoft Windows versions. RasMol 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. The program has been developed
at the University of Edinburgh's Biocomputing Research Unit and the
Biomolecular Structure Department at Glaxo Research and Development,
Greenford, UK. This latest version is has a significant number of
improvements over RasMol 2.4. In addition to performance improvements and
bug fixes, the major enhancements are described at the end of this message.
For a complete list of changes refer to the distribution's "ChangeLog".
RasMol reads in molecular co-ordinate files in a number of formats and
interactively displays the molecule on the screen in a variety of colour
schemes and representations. Currently supported input file formats include
Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats,
Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer
Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity
information and/or secondary structure information is not contained in the
file this is calculated automatically. The loaded molecule may be shown as
wireframe, cylinder (Dreiding) stick bonds, alpha-carbon trace, spacefilling
(CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons
or parallel strands), hydrogen bonding and dot surface. Atoms may also be
labelled with arbitrary text strings. Different parts of the molecule may be
displayed and coloured independently of the rest of the molecule or shown in
different representations simultaneously. The space filling spheres can even
be shadowed. The displayed molecule may be rotated, translated, zoomed,
z-clipped (slabbed) interactively using either the mouse, the scroll bars,
the command line or an attached dials box. RasMol can read a prepared list
of commands from a `script' file (or via interprocess 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 both raster and vector PostScript, GIF, PPM, BMP, PICT,
Sun rasterfile or as a MolScript input script or Kinemage.
RasMol will run on a wide range of architectures and systems including
SGI, sun4, sun3, sun386i, DEC, HP and E&S workstations, IBM RS/6000,
Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC (under
Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple
Machintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows).
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 rendering
(via the XInput and MIT-SHM extensions) if available.
The source code is public domain and freely distributable provided that
the original author is suitably acknowledged. The complete source code and
user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk
[184.108.40.206] in the directory /pub/rasmol. The source code, documentation
and Microsoft Windows executables are stored in several files appropriate
for the receiving operating system. Please read the "README" file in the
distribution directory. UNIX and VAX systems should retreive either
RasMol2.tar.Z, RasMol2.tar.gz. Apple Mac users should retrieve rasmac.sit.hqx.
Microsoft Windows users should retrieve raswin.zip and optionally the Visual
Basic package rasmenu.zip. All these files include source code, on-line help,
user manual and reference card. RasMac.sit.hqx, RasWin.zip and RasMenu.zip
also contain executables for the required platform. Please remember to use
"binary" mode when transferring these files between systems. Check that the
file size is the same before and after transfer.
Any comments, suggestions or questions about the package may be directed
to the author at "rasmol at ggr.co.uk".
Enhancements since Version 2.4 [June 1994]
o Developed an Apple Machintosh version of RasMol. `RasMac' requires
System 7.0 or later and can compile under Symantec C/C++ or Metrowerks
C/C++ compilers for either the 68k or PPC. A `fat' binary is included
in the Machintosh distribution. RasMac can be used under MacMosaic.
o Implemented atom labelling, any atom (or set of atoms) may be labelled
by an arbitrary text string. Embedded characters allow the display of
atomic symbol, residue name, residue number, atom name etc...
o Added support for the entire periodic table of elements. In addition
to VdW radii and CPK colours this allows atoms to be selected by name,
e.g. "select copper,zinc", and by atomic number, "select elemno>=35".
o Improved the algorithms used to determine connectivity. RasMol now
uses the covalent radius of each element to determine bonding for
`small molecules'. The algorithm used may be selected with the
"connect" command. This also fixes problems reading CONECT records
in non-standard PDB files and allows PDB files to specify bond order.
o RasMol now allows distances and radii to be given in Angstroms if
they contain a decimal point. Non-integer values may also be given
to the "slab", "zoom", "rotate" and "translate" commands.
o Added the ability to generate Kinemage format files for display in
David Richardson's Mage program (as distributed by Protein Science).
Added the ability to generate Apple PICT files on all platforms.
o Add the "colour atoms charge" and "colour dots potential" to colour
code atoms by their charge and dot surfaces by their electrostatic
potential respectively. [For files containing charge information!]
o Improved the X Windows user interface using Motif-style pull-down
menus instead of buttons. Added (improved) support for SGI's hardware
o Significantly reduced the size of generated RasMol scripts. The "save"
and "write" commands no longer work in scripts to be safe under Mosaic.
Roger Sayle, INTERNET: ras32425 at ggr.co.uk
Glaxo Research & Development (GRD) ros at dcs.ed.ac.uk
Greenford Road, Greenford Tel: (+44) 081 966 3567 (direct line)
Middlesex UB6 0HE, UK. Fax: (+44) 081 966 4476