RasMol 2.3 Molecular Graphics Package Available

RasMol Molecular Graphics rasmol at dcs.ed.ac.uk
Mon Mar 7 13:25:06 EST 1994



                            RasMol 2.3
              Molecular Graphics Visualisation tool.

                           Roger Sayle 
                   BioMolecular Structure Group
                   Glaxo Research & Development
                     Greenford, Middlesex, UK.
                          February 1994


    This posting is to announce the public release of RasMol 2.3 molecular
graphics visualisation program.  This package has been developed at the
University of Edinburgh's Biocomputing Research Unit over the last few 
years, and more recently with financial assitance from a visiting position 
at Glaxo Research and Development. This latest version has a significant 
number of improvements over RasMol 2.2. 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 is an X Window System tool intended for the visualisation of 
proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) 
files and interactively renders them in a variety of formats on either an 
8bit or 24/32bit colour display. The complete source code and user 
documentation for the UNIX/X11, IBM PC/MSWindows and the VMS/DecWindows
versions may be obtained by anonymous ftp from ftp.dcs.ed.ac.uk 
[129.215.160.5] in the directory /pub/rasmol. All the source code is
contained in the file RasMol2.tar.Z and the MS Windows source code and
executable in the file raswin.zip. Both of these files include on-line 
help, hypertext documentation and the previous (dated) version of the 
PostScript user reference manual.

    Please remember to use "binary" mode when transferring files between 
UNIX and MSDOS systems. Check that the file size is the same before and
after transfer. The MSWindows error "No Memory for Application" is
symptomatic of transfering "raswin.exe" in ASCII mode (corrupting it).

    The program is intended for teaching and generating publication 
quality images. The program has both a menu system and a full featured
command line interface. Different parts and representations of the 
molecule may be coloured or displayed in a number of formats independently.
Currently supported formats include wireframe, ball and stick, backbone,
space filling spheres and solid or strands ribbon models. The space filling 
spheres may even be shadowed. The molecule may be manipulated using the
mouse, the scroll bars, the interactive command line or from a dials box 
(if one is attached). The resulting image may be saved at any point in 
PostScript, GIF, PPM, Sun rasterfile or Microsoft BMP formats.  For more 
details see the RasMol reference manual. On a SparcStation, it can shadow 
a 10,000 atom spacefilling protein in less than 10 seconds.

    The current version of the program has been tested on sun3, sun4, 
sun386i, SGI, DEC & E&S mips based machines, DEC Alpha (OSF/1 and OpenVMS),
VAX VMS (under Dec Windows), IBM RS/6000, hp9000, sequent and IBM PC running
both Linux, BSD386 and *BSD compiled under both gcc and (usually) the native 
compiler. The Microsoft Windows version requires version 7 of the Microsoft 
Optimizing C Compiler or the Visual C++ Compiler and the Microsoft Software 
Development Kit (SDK). 

    The source code is public domain and freely distributable provided that
the original author is suitably acknowledged. 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 2.2 [October 1993]

  o The mouse can now control X, Y and Z rotations, X and Y translation,
    zooming (scaling) and the Z-clipping plane (slabbing). Mouse bindings
    may be controlled by the "set mouse" command with the parameters
    "rasmol", "insight" or "quanta". The "rasmol" bindings are suitable
    for two button mice.

  o Maximum magnification is now dependent upon the size of the molecule,
    allowing magnification by more than 200%. The RasMol "centre" command 
    allows the molecule to rotate about a given atom (or centre of gravity 
    of an arbitrary set of atoms). The RasMol "reset" command returns the 
    viewing transformation to its initial default values.

  o RasMol now draws ribbon diagrams of nucleic acids (both DNA and RNA).
    There is also a (developmental) "set ribbons solid" command (and
    corresponding "set ribbons strands") that displays ribbons as
    normal shaded triangles. The command "colour structure" now colours 
    proteins by secondary structure assignments.

  o RasMol will now read in compressed files (either UNIX compress .Z
    or GNU gzip .z or .gz) decompressing the file automatically. There
    is also an environment variable (RASMOLPDBPATH) to set the default
    file search path (for example pointing to the Brookhaven CD path).
    RasMol now performs '~' expansion on filenames. Filenames no longer
    need be surrounded in quotes.

  o RasMol has been completely ported to VAX/VMS, using ASTs to multiplex
    input signals rather than the UNIX select(2) system call. The VMS
    version doesn't (yet) support file decompression, file path searching 
    or the X11 shared memory extension.

  o The UNIX man pages and on-line help have been substantially rewritten.
    This information is now available as hypertext under Microsoft Help 
    (in Windows 3.1) and under "mosaic" in HTML (if you have NCSA's WWW
    viewer).
    
  o There are a number of experimental/development extensions to the RasMol
    "write" command. The "write script" command saves the current viewpoint
    and rendering options (but not yet the molecule representation) to a 
    RasMol "script" file. The "write molscript" command generates a MolScript
    script file of the protein from the current viewpoint with the 
    appropriate secondary structure assignments (but not yet the scaling,
    clipping or representation). The "write vectps" command saves the
    current image as `vector' PostScript commands rather than as a PostScript
    `image' raster bitmap.

  o RasMol now registers itself as a Tcl/Tk client to allow interprocess
    communication. An improved Tk Graphical User Interface will be 
    distributed with RasMol 3.0. Several improvements have been made to
    the existing menu system.

  o Added the predefined sets "water", "ion", "solvent", "ligand" and
    "bonded". RasMol defaults to "backbone" representation when loading
    files containing no bonded atoms [alpha carbon position only PDB files]

  o Added the RasMol "renumber" command to force sequential number of
    macromolecule chains.

-- 
Roger Sayle, Protein Biochemistry,    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 0AG, UK.                Fax:   (+44) 081 423 4070



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