ChangeLog 4


[06/06/94]    RS    raswin.c rasmol.h molecule.c render.c
        Completed port of RasMol v2.4 to Windows NT. Thanks to
        David Stranz and David Digby.

[05/06/94]    RS    outfile.c
        Corrected bug in generating Vector Postscript in RasWin,
        resulting in the image appearing inverted on the page.
        Thanks to Tomasz Heyduk.

[01/06/94]    RS    raswin.c raswin.rc raswin.idm
        Added CHARMm format files to the RasWin file open dialog box
        and added the "Strands" menu item to the "Display" menu.

[01/06/94]    RS    outfile.c transfor.c transfor.h
        Optimised representation of molecule in generated RasMol
        script files by detecting "cpk" colours and VdW radius.

[31/05/94]    RS    outfile.c
        Added complete support for writing out the current molecule
        representation in a RasMol script file using "write script".

[31/05/94]    RS    molecule.c transfor.c
        Improved lazy calculation of hydrogen bonding and disulphide
        bridges, hence "hbonds off" and "colour hbonds none" no longer
        force evaluation.

[27/05/94]    RS    command.c render.c transfor.c
        Modified the DisplayRibbon routine to allow the simultaneous
        display of strands and ribbons. Removed the "set ribbons"
        command and replaced it with "ribbons" and "strands".

[26/05/94]    RS    transfor.c render.c
        Changed the way that ribbons are selected and rendered in
        different colours. This brings the ribbon rendering in line
        with alpha carbon position and colouring.

[23/05/94]    RS    molecule.c
        Corrected bug in LoadAlchemyMolecule that resulted in molecules
        having the wrong chirality. Thanks to Mikhail Matrosovich.

[20/05/94]    RS    outfile.c
        Improved the Molscript script file interface. The RasMol
        "write molscript" command now stores the scaling, translation
        and slabbing (z-clipping) information. Thanks to Kevin Gardner.

[20/05/94]    RS    raswin.c
        Corrected bug that caused the DIB copied to the clipboard or
        DDE'ed to another application to have the wrong colour map.

[19/05/94]    RS    molecule.c
        Corrected bug in RasMol that caused it to report far too many
        ladders in DSSP. Changed references to "Ladders" to "Strands".

[19/05/94]    RS    molecule.c molecule.h command.c tokens.h
        Added support for CHARMm format co-ordinate files. Thanks to
        Charles Brooks.

[18/05/94]    RS    molecule.c
        Removed interchain bonding. This makes loading a multi-chain
        protein faster and allows for RMS fitting with RasMol.

[18/05/94]    RS    command.c tokens.h transfor.c transfor.h render.c
        Added a second colour to RasMol strands ribbons. Hence, the
        command "colour ribbons1 blue" and "colour ribbons2 red"
        draws blue ribbons with the outmost stands in red.

[17/05/94]    RS    command.c render.c render.h
        Renamed the command "set dots" to "set radius" and added the
        command "set solvent" which controls the dot surface as
        either VDW or solvent accessible. The radius controls either
        the VDW radius or the Solvent Probe Sphere radius.

[16/05/94]    RS    raswin.c
        Added scroll bar and terminal history to the RasMol command
        line window. Improved scrolling in resized windows.

[12/05/94]    RS    raswin.c rasmol.c mswin31.c transfor.c
        Corrected bug in RasMol that resulted in the "specular",
        "specpower" and "ambient" parameters not being reset by a
        RasMol "zap" command and fixed initial RasWin CMap.

[12/05/94]    RS    command.c tokens.h abstree.c abstree.h
        Added the atom property "elemno" that uniquely identifies
        each atoms element type, hence "select elemno=26" identifies
        all sulphur atoms.

[12/05/94]    RS    molecule.c
        Added a test to check if the PDB x, y and z co-ordinates of
        an atom are 9999.000 indicating an XPLOR pseudo atom. Thanks
        to Chris Littler and Harren Jhoti.

[11/05/94]    RS    command.c render.c render.h
        Added the command "set dots <value>" to set the probe
        sphere radius for calculating the solvent accessible
        surface of a protein.

[11/05/94]    RS    render.c
        Corrected bug when drawing thin cylinders since the change
        to DrawTwinLine for axes, bounding box and unit cell.

[10/05/94]    RS    raswin.c
        Corrected bug in the DDE formating of the picked atoms

[10/05/94]    RS    molecule.c
        Fixed bug in RasMol that incorrectly determined the lowest
        residue number in PDB files that are unordered. Thanks to
        Ken Davis.

[09/05/94]    RS    molecule.c molecule.h command.c render.c tokens.h
        Fully implemented the RasMol commands "set unitcell" and
        "show symmetry", these now take the crystal symmetry
        information from the CRYST1 record of a PDB file.

[03/05/94]    RS    render.c
        Corrected RasWin problem in DisplayRibbon caused by rounding
        when interpolating Z-coordinates with large ZOffset.

[03/05/94]    RS    transfor.c
        Corrected RasWin overflow bug in ScaleColourAttrib that
        caused `hot' atoms to be displayed black instead of red.

[03/05/94]    RS    rasmol.doc
        Corrected several typographic mistakes and errors within
        the rasmol documentation. Thanks to Naoum Salame.

[29/04/94]    RS    raswin.c mswin31.c
        Managed to trace a RasWin colour map initialisation problem
        that occasionally caused RasWin to crash with a GDI error or
        start with wrong colour background. Thanks to Dave Digby.

[28/04/94]    RS    x11win.c
        Corrected buffer char types in x11win.c that were causing
        warnings on pedantic compilers. Thanks to Ethan Merritt.

[20/04/94]    RS    outfile.c
        Added support for vector PostScript output of dot surfaces.

[20/04/94]    RS    render.c render.h command.c transfor.c transfor.h
        Added a Van der Waals dot surface representation to RasMol.
        The command "dots <boolean>" enables and disables a dot
        surface of the currently selected atoms. "dots <value>" can
        control the dot density, "colour dots" colours the whole
        dot surface a given colour [the default is taken from atoms]

[20/04/94]    RS    rasmol.c
        Corrected bug with including <unistd.h> on Evans & Sutherland
        ESV workstations.

[19/04/94]    RS    render.c
        Solved a bug in IdentifyAtom that refused to identify picked
        non-connected atoms when bonds are being displayed.

[19/04/94]    RS    molecule.c
        Corrected bug in loading alchemy format files. Atom serial
        numbers were incorrect resulting in incorrect bonding. Thanks
        to Ben Gaskins.

[18/04/94]    RS    render.c render.h tokens.h command.c
        Added the commands "set axes" and "set boundingbox" to display
        the co-ordinate axes and molecule bounding box on screen.

[18/04/94]    RS    pixutils.c
        Corrected bug in routines `ClipLine' and `ClipVector' which
        caused lines that clipped the bottom of the screen to bend.

[18/04/94]    RS    raswin.c
        Corrected bug in the DDE transfer of CF_DIB objects for the
        DDE "Image" item. Thanks to Dave Digby and Ken Davis.

[15/04/94]    RS    rasmol.c raswin.c abstree.h transfor.c molecule.c
        Better support for the display of small molecules. Smaller
        bond cylinder radius for `sticks' images of molecules with
        less than 256 atoms, and use unadjusted Van der Waals radius
        for molecules containing explicit hydrogen atoms.

[15/04/94]    RS    molecule.c
        RasMol now uses the connectivity specified in PDB CONECT
        records when displaying molecules with less than 256 atoms,
        i.e. small compounds. Thanks to Brian Dunford-Shore.

[14/04/94]    RS    rasmol.h raswin.c
        Extended the range of items exported by DDE to include the
        picked atom's co-ordinates and the image being drawn on
        the screen (transfered as CF_DIB).

[13/04/94]    RS    raswin.c
        Improved the processing of WM_SIZE handling by increasing
        XRange to be long aligned rather than decreasing it. This
        avoids the occasional black line down the side of the screen.

[13/04/94]    RS    transfor.c
        Corrected bug in transfor.c that cleared more entries in
        in the StructShade table than there were. This sometimes
        caused RasMol to crash later during keyword lookup.

[12/04/94]    RS    rasmol.c
        Changed the TERMIOS handling section to support FreeBSD1.1
        using XFree2.x. Special thanks to Pedro A M Vazquez.

[11/04/94]    RS    molecule.c
        Corrected bug in RasMol that caused residues with different
        insertion codes to be placed in the same group. They're now
        placed in consecutive Groups but with the same serial number
        hence may be "renumbered". Thanks to Anne Cleasby.

[07/04/94]    RS    molecule.c
        Corrected bug in sizing molecule read from an MDL Mol file.

[05/04/94]    RS    molecule.c molecule.h command.c tokens.h raswin.c
        Added support for reading in files in Molecular Design Ltd's
        (MDL) Mol file format.

[30/03/94]    RS    rasmol.doc
        Corrected HTML bug that caused the NCSA PC Mosiaic viewer to
        crash when displaying rasmol.html.

[28/03/94]    RS    pixutils.c
        Corrected a bug in RenderPolygon that caused a floating point
        division by zero error and huge/far segment problems on the
        IBM PC.

[25/03/94]    RS    outfile.c
        Finished implementing correctly intersecting spheres when
        outputing vector postscript. However, this may cause
        problems for low memory laser printers.

[23/03/94]    RS    transfor.c
        Corrected bug that set the default scale too large for very
        small molecules.

[22/03/94]    RS    molecule.c
        Handle incompletely specificed @<TRIPOS>MOLECULE records in
        Sybyl Mol2 files such as those exported from InSight. Handle
        `small molecule' atom names (containing serial numbers) in
        PDB files. Thanks to Martin Hargreaves

[18/03/94]    RS    pixutils.c
        Improved the polygon rendering algorithm. RasMol now displays
        solid ribbons as gouraud rather than constant normal shaded

[18/03/94]    RS    rasmol.c
        Added the command line options "-pdb", "-alchemy", "-mol2"
        and "-xyz" to specify the format of the file given on the
        command line.

[17/03/94]    RS    molecule.h command.h
        Increased the maximum filename length from 80 to 256 chars.

[15/03/94]    RS    outfile.c outfile.c command.c
        Improved the quality of "vectps" output. RasMol now correctly
        handles intersection of spheres in vector PostScript output.
        The use of `cartoon' outlines is now controlled by the
        "set vectps <boolean>" command.

[14/03/94]    RS    x11win.c
        Change Visual detection code for 24bit and 32bit displays to
        support both TrueColor and DirectColor. This adds support for
        the HP 735 CRX-24. Special Thanks to Thomas Lew.

[11/03/94]    RS    outfile.c
        Improved speed of vector PostScript printing by performing
        sphere and bond culling before sorting/generating output.

[11/03/94]    RS    molecule.c molecule.h command.c tokens.h raswin.c
        Added support for MSC XMOL's XYZ format files.

[10/03/94]    RS    molecule.c molecule.h command.c tokens.h raswin.c
        Added support for Sybyl .mol2 file format for reading in
        a file (i.e. "load mol2"). Read small molecule connectivity
        from "alchemy" and "mol2" files, if it exists.

[09/03/94]    RS    x11win.c
        Allow the EIGHTBIT version of RasMol to display on 8-bit
        grey-scale X displays. Special thanks to Gerald Loeffler.

[09/03/94]    RS    molecule.c
        Allow backbone traces to be drawn to unknown residues
        that contain an alpha carbon.

[04/03/94]    RS    !Announced the public release of RasMol and
        RasWin version 2.3, available by anonymous FTP from [] in the directory
        /pub/rasmol. The announcement was made in both, bionet.announce,,
        sci.chem, newsgroups.