RasMol 2.5 Molecular Graphics Visualisation tool. Roger Sayle BioMolecular Structures Group Glaxo Research & Development Greenford, Middlesex, UK. October 1994 This posting is to announce the release of RasMol version 2.5. This latest version is available for the Apple Macintosh 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 Macintosh (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 [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. 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@ggr.co.uk". Enhancements since Version 2.4 [June 1994] o Developed an Apple Macintosh 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 Macintosh 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 dials boxes. 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 -- Roger Sayle, INTERNET: ras32425@ggr.co.uk Glaxo Research & Development (GRD) ros@dcs.ed.ac.uk Greenford Road, Greenford Tel: (+44) 081 966 3567 (direct line) Middlesex UB6 0HE, UK. Fax: (+44) 081 966 4476