ChangeLog 6


[05/05/95]    RS    render.c
        Corrected 16bit precision problem with cartoons on PCs and
        Macintoshes. These caused rounding errors in `ribbons'.

[02/05/95]    RS    INSTALL
        Added additional build info for RasMac on the PowerPC using
        Metrowerks C++ v1.2. This requires additional files to v1.1.
        Special thanks to Graham Palmer.

[03/04/95]    RS    pixutils.c pixutils.h render.c command.c
        Added the ability to display dashed "strands" ribbons.

[03/04/95]    RS    render.c
        Modified the handling of the first and last residue in
        a chain to only extend to the alpha carbon except when
        the last residue is an arrow head.

[27/03/95]    RS    render.c
        Fixed bug in cartoon representation when final residue in a
        chain is a beta-sheet. Improved "CalculateInten" performance.

[27/03/95]    RS    rasmol.c
        Made several changes to rasmol.c to allow RasMol to compile
        with DEC C (on AXP and VAX) without /standard=vaxc. Special
        thanks to Martin Zinser.

[26/03/95]    RS    render.c render.h pixutils.c pixutils.h command.c
        Added the new representation "cartoon" which represents a
        protein as a Richardson-style cartoon. The width of the
        cartoon is given as a parameter, the depth of the ribbon
        and use of arrow heads may be changed using "set cartoon".

[25/03/95]    RS    render.c command.c transfor.c molecule.h
        Changed the semantics of the "trace" command and added a
        new representation, "trace" which displays a cylindrical
        spline representation of "backbone".

[22/03/95]    RS    render.c render.h command.c tokens.h transfor.c
        Added the "Monitor" representation to RasMol as an dashed
        line between two atoms, optionally labelled by the distance
        between the atoms (the default).

[16/03/95]    Makefile
        Added comments about use of +O4 optimisation using HPUX 9.05
        on the native PA-RISC compiler. Thanks to Richard Mathar.

[13/03/95]    RS    outfile.c
        Implemented dashed lines in RasMol's vector PostScript output.
        This now includes the ability output of hbonds and ssbonds.

[13/03/95]    RS    script.c
        Fixed bug when generating RasMol scripts caused by overlapping
        datum type masks. This caused errors with dashed vectors.

[12/03/95]    RS    x11win.c
        Fixed a problem using scroll bar arrows to spin a molecule
        with three-button emulation on XFree (Linux and NetBSD).

[07/03/95]    RS    render.c
        Improved performance of "isqrt" routine, the most frequently
        called function when rendering ribbons.

[06/03/95]    RS    render.c
        Implemented the routine "InitialiseTables" to avoid using
        "isqrt". This drastically reduces the start-up time.

[06/03/95]    RS    render.c
        Improved rendering of double & triple bonds.

[03/03/95]    RS    command.c render.c render.h pixutils.c
        Added the ability to display double and triple bonds as
        two and three lines using the "set bonds true" command.

[03/03/95]    RS    command.c tokens.h render.c transfor.c script.c
        Added the ability to display bonds and backbones as dashed
        lines using either the "dashes" command or the "dashes"
        parameter to the "wireframe" and "backbone" commands.

[03/03/95]    RS    command.c
        Modified 'FetchFile' to display explicitly specified
        hydrogen bonds by default.

[03/03/95]    RS    pixutils.c
        Improved quality of dashed lines.

[02/03/95]    RS    render.c molecule.c transfor.c transfor.h
        Ported RasMol to compile under Borland's Turbo C/C++. This
        required rewrite of ClearBuffers to avoid "_fmemset" bug.

[02/03/95]    RS    outfile.c outfile.h command.c tokens.h x11win.c
        Added support for Silicon Graphics' IRIS RGB format image
        files for both 8 and 32bit versions, "write iris <filename>".

[01/03/95]    RS    outfile.c
        Tidied up many of the image file output routines.

[28/02/95]    RS    molecule.h abstree.c abstree.h
        Improved handling of RNA bases and conversion of non-standard
        nucleotide atom names. Thanks to Hans Hoppe.

[17/02/95]    RS    molecule.c
        Finally implemented internal to cartesian co-ordinate
        conversion for MOPAC internal input files. Very special
        thanks to Klaus-Peter Gulden.

[16/02/95]    RS    molecule.c
        Added detection of MOPAC file types, and added support
        for MOPAC cartesian co-ordinate input files.

[15/02/95]    RS    molecule.c
        Added support for reading MOPAC output files including
        charge information (provided the job doesn't use the
        "NOXYZ" keyword as an option).

[14/02/95]    RS    render.c
        Added "X", "Y" and "Z" axes labels to the "set axes on"

[13/02/95]    RS    render.c render.h command.c
        Implemented the "set picking centre" command to allow the
        centre of rotation to be selected by clicking on an atom.

[10/02/95]    RS    render.c render.h pixutils.c pixutils.h command.c tokens.h
        Started adding more support for RasMol stereo viewing.
        Stereo is enabled by either "stereo on" or "set stereo on".

[10/02/95]    RS    pixutils.c
        Improved performance of function DisplayString avoiding
        clipping and reduced intensity of atom labels.

[09/02/95]    RS    abstree.c
        Implemented function 'CalcTorsion' for "set picking torsion".

[06/02/95]    RS    render.c
        Increased the maximum sphere rendering radius within RasMol.
        This is the first step to producing high-resolution output.

[02/02/95]    RS    abstree.c abstree.h command.c tokens.h
        Added support for selecting individual models in "nmrpdb"
        files, either use "model=25" property or expression "::25".
        RasMol also now allows chains to be specified ":a" and ":1".

[01/02/95]    RS    outfile.c
        Modified the vector Postscript output routines to saturate
        sphere colouring following "set ambient 100".

[23/01/95]    RS    abstree.c
        Added the "%m" label format specifier for amino acid codes.

[20/01/95]    RS    render.c render.h rasmol.c x11win.c
        Added the menu option "Labels" to RasMol for easy labelling.
        Improved internal label handling.

[20/01/95]    RS    abstree.c
        Made functions CalcAngle and CalcDistance more robust.

[18/01/95]    RS    transfor.c transfor.h command.c command.h
        Modified the RasMol "restrict" command to disable the display
        of backbone, ribbons and strand representations. Labels??

[18/01/95]    RS    script.c
        Corrected bug in Kinemage format output that occurred when
        bonds were displayed in some chains but not in others. Also
        fixed potential problems with backbone DNA hydrogen bonds
        in Kinemage files. Thanks to Piotr Zimniak.

[18/01/95]    RS    command.c render.c x11win.c rasmac.c raswin.c abstree.
        Added the options "distance", "angle" and "torsion" to
        the RasMol "set picking" command to inspect geometry.

[17/01/95]    RS    command.c tokens.h render.c render.h
        Added the RasMol command "set picking" with options "none",
        "ident" (default) and "label". The final option toggles the
        display of atom labels on the picked atom.

[13/01/95]    RS    command.c
        Added the "set write" command to allow "write" and "save"
        commands to work from the command line.

[13/01/95]    RS    command.c tokens.h x11win.c
        Added "refresh" command to update screen from script file.

[12/01/95]    RS    render.c
        Modified DrawRibbon to use divisons rather than right shifts.
        This corrects problems on Convex. Thanks to Andy Quick.

[06/01/95]    RS    molecule.h molecule.c abstree.c render.c transfor.c
        Modified the "Atom" structure definition to contain atomic
        number, this allowed correct determination of Brookhaven
        NAD and CoenzymeA elements by changing GetElemNumber().

[16/12/94]    RS    raswin.c raswin.rc raswin.idm rasmac.c
        Modified the menu ogranisation of RasWin to include an Edit
        menu containing "Select All" and a "Print SetUp..." option.

[16/12/94]    RS    molecule.c
        Corrected bug reading CHARMm format files that sometimes
        placed different residues in separate chains. Thanks to
        Stefan Fischer.

[15/12/94]    RS    script.c
        Fixed bug in WriteMolScriptFile that occasionally resulted
        in all residues additionally being displayed as coil.

[13/12/94]    RS    molecule.c molecule.h command.c rasmol.c raswin.c
        Added the "nmrpdb" file format to allow all NMR conformations
        to be loaded into RasMol into different `models'.

[08/12/94]    RS    command.c
        Corrected a bug in command.c that resulted in an error if
        a label string wasn't placed between string terminators.

[08/12/94]    RS    rasmol.c
        Corrected bug in RasMol performance profiling routines.

[08/12/94]    RS    x11win.c
        Improved support for monochrome X. The improved performance
        algorithm now performs bidirectional error diffusion and
        correctly handles Black/White bit variations (e.g NEC & SUN).

[30/11/94]    RS    molecule.c
        Modified LoadAlchemyMolecule and ConnectAtoms to enable
        hydrogen bonding to be specified in Alchemy format files.
        Fixed bug with bond types. Thanks to Chris Wilson.

[30/11/94]    RS    outfile.c
        Changed the creator and file type of PostScript files on
        the Mac to 'vgrd' and 'TEXT' respectively. This enables
        printing by Apple's PostScript utility. Thanks to Tom Jovin.

[29/11/94]    RS    x11win.c
        Added support for Monochrome only X Windows displays by
        dithering 8bit images before calling XPutImage. The current
        error term diffusion algorithm may have to be improved for
        wireframes and dot surfaces. Thanks to Cheuk-san Edward Wang.

[28/11/94]    RS    molecule.c
        Made several changes to RasMol to account for unconventional
        atom naming in PDB files, such as strange hydrogens 'HD',
        'HG' and 'HH' and cysteine sulphurs ' SB1'. Thanks to Bruce

[28/11/94]    RS    rasmol.doc
        Added "primitives" to the keyword list in the on-line help
        documentation to solve xref `bug'. Thanks to Steve Brenner.

[21/11/94]    RS    molecule.c
        Changed the handling of PDB residue synonyms to make name
        comparison more efficient. Added synonyms for standard
        nucleic acids. Thanks to Hans Hoppe.

[21/11/94]    RS    rasmol.c
        Corrected problem with the static forward declaration
        of HandleEvents that caused problems on IRIX 4.0 compilers.
        Thanks to Noham Weinberg.

[16/11/94]    RS    rasmol.c command.c
        Implemented the "Save As..." option on the File Menu in
        the UNIX version of RasMol. Thanks to Henry Rzepa.

[11/11/94]    RS    molecule.c
        Added the ability to read in connectivity records from
        columns 32 and 37 of PDB's CONECT records. These are used
        by some programs for heavy elements instead of hbonds!

[10/11/94]    RS    abstree.h
        Corrected errors in the covalent radii of several of the
        heavy elements in the periodic table.

[08/11/94]    RS    molecule.c
        Corrected a bug in FindSybylResNo that resulted in the wrong
        atom types being found in Mol2 files. Thanks to Jim Bentley.

[08/11/94]    RS    rasmol.h outfile.c
        Corrected problem with undefined _fstricmp in raswin.c and
        funtion WriteIRISFile under Windows NT. Thanks to Pedro Mendes.

[08/11/94]    RS    descrip.mms
        Corrected several typos. Thanks to Ulrich Schmitt.

[08/11/94]    RS    render.c script.c
        Fixed bug in RasMol that resulted in a division by zero
        when "set unitcell on", but the PDB file contains no
        crystal unit cell information. Thanks to Arne Eofsson.

[01/11/94]    RS    pixutils.c
        Corrected bug in routines SolidRibbon and StrandRibbon
        that didn't specify __far pointers to Knots despite the
        defintion in pixutils.h. Announced RasWin version 2.5.1!

[28/10/94]    RS    !Announced the public release of RasMol, RasMac
        and RasWin version 2.5, available by anonymous FTP from [] in the directory
        /pub/rasmol. The announcement was made in,
        bionet.announce,, sci.chem,, bionet.xtallography
        and sci.techniques.xtallography newsgroups.