RasMol 2.4 Molecular Graphics Package Available

RasMol Molecular Graphics rasmol at dcs.ed.ac.uk
Thu Jun 9 16:41:05 EST 1994


                            RasMol 2.4
              Molecular Graphics Visualisation tool.

                           Roger Sayle 
                  BioMolecular Structures Group
                   Glaxo Research & Development
                     Greenford, Middlesex, UK.
                            June 1994


    This posting is to announce the release of RasMol version 2.4. RasMol
is a molecular graphics program intended for the visualisation of proteins,
nucleic acids and small molecules. The program is aimed at teaching, display
and generation of publication quality images. The program has been
developed at the University of Edinburgh's Biocomputing Research Unit and
recently with financial assistance from the Biomolecular Structures Group
at Glaxo Research and Development, Greenford, UK. This latest version has 
a significant number of improvements over RasMol 2.3. Most of these 
enhancements are described at the end of this message. For a complete list 
of additions, bug fixes and acknowledgements, 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 (drieding) stick bonds, alpha-carbon trace, spacefilling
(CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons
or parallel strands), hydrogen bonding and dot surface. Different parts of
the molecule may be displayed and coloured independently of the rest of
the molecule or shown in different representations simultaneously. The
spacefilling 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 be used to create script files 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, Sun rasterfile or as a MolScript input 
script.

    RasMol will run on a wide range of architectures and systems including 
sun3, sun4, sun386i, SGI, DEC, HP and E&S workstations, IBM RS/6000, Cray,
Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), VAX VMS (under DEC 
Windows), IBM RS/6000, HP and IBM PC (under Microsoft Windows, Windows NT,
OS/2, Linux, BSD386 and *BSD). Support for an Apple Machintosh version is
planned for October '94. 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
[129.215.160.5] 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 or rasmol2.zip. Microsoft Windows users should
retrieve RasWin.zip and optionally the Visual Basic package RasMenu.zip 
both of which contain executable .EXE files. All these files include source 
code, on-line help, user manual and reference card. 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 either "rasmol at dcs.ed.ac.uk" or "rasmol at ggr.co.uk".



Enhancements since Version 2.3 [February 1994]

  o Developed an extensive Graphical Uer Interface (GUI) to the Microsoft
    Windows version of the program. This Visual Basic application will 
    shortly be rewritten and integrated into RasMol on MS Windows, X Windows 
    and Apple Mac platforms.

  o Added the ability to store the current representation and transformation
    of the molecule in a RasMol script file using the "write script" command.
    These script files are also edittable by hand and allow presentations 
    and databases of `interactive protein images' to be constructed.

  o Added support for molecular dot surfaces. Dot surfaces may currently
    be displayed on a Van der Waal's or fixed radius surface on the 
    molecule with a specified point density. A partial implementation of 
    solvent accessible dots surfaces initial attempt has been made at 
    supporting solvent accessible surfaces using the "set solvent" command.

  o Allow the simultaneous display of biomolecular ribbons as both smooth
    solid surfaces and as parallel depth-cued strands. Solid ribbons are 
    now Gouraud rather than flat (normal) shaded. Allow the central and
    outermost strands of a ribbon to be displayed in different colours.

  o Support for a number of small molecule file formats including CHARMm,
    MDL Mol files, Sybyl Mol2 and MSC's (XMol) XYZ format. Smaller default 
    bond radius for stick models of small molecules and unadjusted Van der 
    Waals radii of atoms in molecules containing explicit hydrogen atoms.

  o Improved the quality of MolScript script file output. In addition to
    rotation and secondary structure, RasMol now also passes zooming,
    translation and z-clipping information to MolScript.

  o Improved the methods used to determine molecule bonding. RasMol now
    honours connectivity records stored in co-ordinate files if included.

  o RasMol can now also display the cartesian co-ordinate axes, bounding 
    box and crystallographic unit cell of the displayed molecule.

  o Improved the resizing of the Microsoft Windows command line window 
    and added a scroll bar to redisplay text past the top of the screen.

-- 
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




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