ChangeLog 1

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[08/10/93] RS molecule.c
Solved problem with protein hydrogen bonding, in PDB files
containing both protein and nucleic acid sequences.
[07/10/93] RS outfile.c
Corrected problem with compressed postscript output using
"colour" instead of "color" resulting in monochrome output.
[06/10/93] RS abstree.c rasmol.c render.c
Moved #include <stdlib.h> inside the #ifdef IBMPC to avoid
compilation errors on SUN 386is without stdlib.h!
[05/10/93] RS command.c abstree.c
Added support for negative residue numbers when specifing
single residue numbers and ranges of residues, and allow the
use of negative numbers in RasMol conditional expressions.
[05/10/93] RS rasmol.c molecule.h
Altered the main loop of RasMol and the way char arrays are
initialised in molecule.h to avoid compilation warnings with
SGI's cc compiler. Thanks to Lachlan Bell (lhb@seqnet.dl..).
[04/10/93] RS Makefile Imakefile
Added a comment to the Makefile to the effect that the Xinput
library is linked using -lXi instead of -lXinput on SGIs.
[01/10/93] RS molecule.c render.c
Modified bug in molecule.c that only created new groups or
chains at changes in PDB residue serial numbers. This caused
ribbon problems on some GAP3.pdb. Thanks to Andrew Coulson.
[29/09/93] RS molecule.c
Changed method for determining hydrogen bond offests for the
RasMol "colour hbond type" command to not use the residue
serial numbers found in the PDB file.
[29/09/93] RS molecule.c molecule.h render.c
Recorded breaks in protein backbone caused by large alpha
carbon separation to avoid drawing ribbon over chain breaks.
[27/09/93] RS x11win.c
Improved the scroll bars to allow the `button' to be dragged
by moving the mouse whilst a button is depressed.
[27/09/93] RS molecule.c
Added a flag to indicate the source of the current secondary
structure assignment used by the program, i.e PDB vs DSSP.
[27/09/93] RS rasmol.c raswin.c raswin.rc raswin.idm command.c transfor.c
Replaced "Ball & Wire" with "Ribbons" on the display menu
and improved the way representations are enabled and disabled.
[24/09/93] RS molecule.c tokens.h command.c
Modified LoadPDBMolecule to read the secondary structure
assignment records (HELIX and SHEET) and use these as default
secondary structure assignments when they are present. Added
the command "structure" to force the use of DSSP definitions.
[24/09/93] RS molecule.c
Optimised Implementation of Kabsch and Sander's algorithm to
determine beta sheet secondary structures, reducing time to
analyse GLS2 from over two hours to 7mins on a sun4.
[23/09/93] RS abstree.c
Modified EvaluateProperty to test amino acid properties by
using an array containing a bitvector of properties for each
amino acid. This is both faster and easier to maintain.
[23/09/93] RS molecule.c command.c tokens.h abstree.c abstree.h
Completed prototype beta sheet secondary structure
determination based upon the Kabsch and Sander's algorithm.
Added the predicate "sheet" for amino acids in ladders.
[23/09/93] RS molecule.c molecule.h transfor.c abstree.c
Added pyrrolidine carboxylic acid and hydroxyproline (and
ASX and GLX) to the list of recognised amino acids for
determining hydrogen bonding and structure determination.
[22/09/93] RS molecule.c molecule.h tokens.h command.c render.c
abstree.c
Corrected bug with RasMol that caused proteins with actyl
N-terminii not to be recognised as amino acid sequences.
Added the predicate "protein" which is the set "amino" and
the n-terminal acetic acid. Thanks to Andrew Coulson.
[21/09/93] RS transfor.c transfor.h
Solved remaining problems with huge proteins in RasWin.
[21/09/93] RS molecule.c
Improved the performance of (helix) secondary structure
determination, by ordering the h-bonds to reduce searching.
[21/09/93] RS molecule.c render.c render.h transfor.c command.c
Modified altered the "Boxing" algorithm used to determine
bonding to use the Shadow tracing hash table. This both
reduces memory and dramatically increases performance
(halving the time to read 2GLS from 43s to 21s on a sun4).
[17/09/93] RS molecule.c molecule.h command.c raswin.c
Solved (some) problems caused by reading in huge proteins
with more than 32767 atoms and bonds, and larger in diameter
than can be represented by 16 bit integers.
[17/09/93] RS render.c
Corrected more problems caused by integer overflow and the
division by zero errors when zooming Ribbon models in RasWin.
[15/09/93] RS command.c
Extended expression syntax to include numbers as primitive
expressions to specify a given residue sequence number. Hence
the "select 5,6" is equiavalent to "select resno=5,resno=6"
and "select 10-20" means "select (resno>=10) and (resno<=20)".
[14/09/93] RS render.c
Corrected problems caused by integer overflow and integral
type conversion warnings with Spline code when zooming.
[13/09/93] RS x11win.c rasmol.h
Added check to the X Window System MIT shared memory extension
to test if server is on the same host (bug in XShm?) and hence
made MITSHM enabled as the default option.
[13/09/93] RS render.c pixutils.c pixutils.h
Completed implementation of ribbons using a MolScript-like
Hermite spline through Carson's control points. Optimized
fixed point implementation and improved ribbon clipping.
[12/09/93] RS render.c transfor.c transfor.h command.c molecule.h
Added an optional width parameter to the "ribbons" command
to allow the user to define ribbon width at each residue
independently, allowing for example wider ribbons in helix.
[12/09/93] RS pixutils.c pixutils.h command.c tokens.h
Added the command "set strands <number>" to allow the user to
globally modify the number strands in ribbon representations.
[29/08/93] RS pixutils.c render.c command.c tokens.h transfor.c
transfor.h
Added prototype support for the RasMol ribbon representation
based on a fixed number of straight strands through Carson's
control points (peptide plane miday between alpha carbons).
[26/08/93] RS raswin.c rasmol.c command.c
Changed the default colour scheme to CPK.
[26/08/93] RS molecule.c
Added support for saving the currently selected atoms and
their connectivity information in an alchemy format file.
[26/08/93] RS x11win.c
Increased the minimum width of the screen to avoid bug in
the X Scroll bar range checking and limit XRange to word
boundaries to solve shared memory bug on some machines.
[25/08/93] RS transfor.c
Changed type of OrigCX, OrigCY and OrigCZ to type Long to
prevent RasWin crashing when loading PDB files centered a
long way from the co-ordinate origin.
[25/08/93] RS x11win.c
Improved code for using MIT's shared memory extension. The
code now uses the XShmCreateImage call and destroys the shmid
to ensure that the shared memory is reclaimed when RasMol is
terminated. Thanks to Andre Beck.
[24/08/93] RS abstree.c
Extended the syntax of primitive atom expressions to allow
the user to select residues (groups) whose names contain non
alphabetic characters, such as digits. Hence the new syntax
allows expressions of the form [SO4]20 and [+U]*P
[24/08/93] RS molecule.c molecule.h render.c transfor.c abstree.c
Added code to determine hydrogen bonding between nucleic
acid residues in distrinct chains. Modified "set hbond
backbone" code, to only draw a single bond between sugar
phosphate backbones for each pair of nucleotides.
[23/08/93] RS transfor.c
Modified the way in which ScaleColourAttrib tries to allocate
the colour map. Now if there are no free shades, it attempts
to allocate as many close matches as possible.
[23/08/93] RS x11win.c
Improved the XInput extensions dials box handling code, to
explicitly check the number of Dials and LEDs present. This
avoids problems on some SGI dials boxes. Thanks to Nick Blom.
[20/08/93] RS molecule.c molecule.h
Added a backbone representation for nucleic acid structures
by connecting sugar phosphate P atoms of consecutive residues.
[20/08/93] RS command.c
Fixed bug caused by "UpdateScrollBars" being called by the
`rotate' command, even when not running interactively.
[20/08/93] RS molecule.c molecule.h tokens.h command.c abstree.c
abstree.h
Added complete code for Kabsch and Sander secondary structure
determination of alpha helices. Added predefined set "HELIX"
that contains all atoms contained in a alpha helix structure.
[19/08/93] RS command.c
Fixed bug in LoadScriptFile that assumed that it was being
called after parsing a command line, causing RasMol to crash
SGI machines that had ".rasmolrc" initialisation files. Thanks
to Peter Murray-Rust and special thanks to Tom Smith!
[19/08/93] RS transfor.c command.c
The restrict command (and hydrogen/hetero menu options) now
removes bonds connected to any removed atom ignoring the
bondmode setting. Isabelle Phan (phan@bioch.ox.ac.uk)
[19/08/93] RS raswin.c
Added Alchemy file type to the RasWin FileOpen dialog box.
[19/08/93] RS molecule.c
Imposed maximum backbone bond length of 7.00 Angstroms.
[18/08/93] RS rasmol.c raswin.c
Modified the actions performed by ReDrawFlag when no
molecule is loaded. This allows the background colour
to be changed before loading a molecule.
[18/08/93] RS x11win.c
Corrected a memory deallocation problem, caused by the
XDestroyImage freeing the current frame buffer. This has
caused numerous untracable errors in previous versions.
[18/08/93] RS abstree.c molecule.c
Added support for IUPAC hydrogen names "1H", "2H" etc...
[10/08/93] RS command.c transfor.c transfor.h molecule.c molecule.h
Added the "colour hbond type" command to enable hydrogen
bonds to be drawn in colours associated with their offsets.
[09/08/93] RS abstree.c abstree.h command.c tokens.h
Completely reorganised the classification of amino acids into
predefined sets. Added sets for "surface" and "buried", for
"small", "medium" and "large" and synonyms "positive" and
"negative" for "acidic" and "basic", the "charged" sets.
[05/08/93] RS molecule.c molecule.h command.c tokens.h
Added support for reading in Alchemy format data files, as
used by the popular PC and Mac program. Thanks to Steve Ludtke.
[05/08/93] RS rasmol.c raswin.c x11win.c mswin31.c command.c
Changed default value of ReDrawFlag to initially be zero
until the molecule is loaded. This corrects bug when the
dispatcher doesn't check stdin when no molecule loaded.
[03/08/93] RS raswin.c mswin31.c
Added Print option to the RasWin file menu to allow the
current image to be printed out using the MS Windows
printer drivers. Tested for Mono & Colour PostScript.
[03/08/93] RS abstree.c
Changed definition of the sets "hydrophobic" and "polar".
Glycine (GLY) is now considered a polar amino acid residue.
[03/08/93] RS rasmol.c x11win.c
Improved dispatch of pending X11 events [RasMol now processes
all X Events until quiescent]. Holding down scroll bar arrow
spins until mouse button released. Fixed server colour search
bug when not running interactively. Thanks to Doug Phillips.
[03/08/93] RS molecule.c
Modified the order in which molecules are internally stored
so saving PDB files preserves the correct atom ordering. Also
solved output chirality problems when INVERT is defined.
[03/08/93] RS outfile.c
Fixed bugs and improved performance of writing output files
under MS Windows caused by rounding when INVERT is defined.
[29/07/93] RS outfile.c
Fixed bug when generating 24bit Run Length Encoded sun
rasterfile format images, thanks to Doug Phillips. Fixed
Monochrome RLE PostScript bug, thanks to Andrew Coulson. Also
changed "64 idiv" to "-6 bitshift" to speed up PostScript.
[28/07/93] RS outfile.c outfile.h command.c rasmol.c raswin.c
Modified the PostScript output routines to include a run
length encoding (RLE) compression option (as default). This
has significantly reduced the size of output files from
several megabytes to a few hundred kilobytes per image.
[27/07/93] RS tokens.h command.c molecule.c molecule.h
Added functions to write out currently selected atoms to a
PDB file as viewed from the current rotation matrix. This
command doesn't output CONNECT, SSBOND or MASTER records
yet. May also add HELIX, TURN and SHEET records in future.
[27/07/93] RS mswin31.c
Corrected bug that resulted in the PixMap image of a molecule
persisting (being redrawn after expose events) after the
molecule has been `closed' or `zapped!'.
[26/07/93] RS !Defined macro "Long" in rasmol.h to be the 32bit
integer type on the current architecture. This should be
defined as long on all architectures except the 64bit
DEC Alpha.
[23/07/93] RS Imakefile
Created Imakefile to allow easy compilation on local machines
using the `xmkmf' command to generate Makefiles with the
appropriate parameters.
[21/07/93] RS bitmaps.h graphics.h transfor.c
Corrected compilation warnings generated by the Solaris v2.0
C Compiler due to default signed chars and ANSI C division.
[08/07/93] RS command.c tokens.h
Changed the way keywords are identified from searching a table
of binary search trees ordered by frequency, to binary search
of an initialised array by token length. This should reduce
both memory and processing time.
[08/07/93] RS abstree.h
Altered the syntax of primitive atom expressions to provide
better support for numeric chain identifiers using optional
colon before chain. CYS11:1 can be distinguished from CYS111!
[03/07/93] RS rasmol.h raswin.c rasmol.c render.c molecule.c
Added support for Dynamic Data Exchange (DDE) of RasMol
parameters and valuation data under MS Windows 3.1.
[02/07/93] RS molecule.c
Corrected a typographical error resulting in molecules being
drawn back to front. This produced images of molecules with
the wrong chirality. Thanks to Pedro Coutinho and Tom Smith.
[01/07/93] RS command.c molecule.c
Solved problems when reading in PDB files that contain no
atoms such as the documentation files cpk.pdb and shapely.pdb.
This allows colour masks to be stored in a separate PDB file
and preloaded before the main molecule. Thanks to Bob Strunz.
[01/07/93] RS graphics.h x11win.c
Added much better support for 24bit and 32bit XVisual display
types. This now permits the 8bit RasMol to run find an
appropriate visual on 24bit and 32bit screens. This solves
problems with obscure default visuals. Special thanks to
Jenny Barna.
[30/06/93] RS command.c abstree.c abstree.c
Implemented the "WITHIN" function in atom expressions. This
selects all atoms within a specified radius of a given set
of atoms (defined by an atom expression). This even permits
the WITHIN command to be used recursively.
[29/06/93] RS x11win.c
Improved the local colour map support for 8bit displays. The
program no detects if the entire global colour map is already
allocated and forces the use of a local colour map. This gets
around the problems of black on black menu bottons and scroll
bars.
[27/06/93] RS command.c transfor.c transfor.h
Implemented the "colour [atom] amino" command that colours
amino acid residues by their properties. These colours are
more intuitive (conventional) than shapely colours and better
for a range of displays. Thanks to Andrew Coulson.
[27/06/93] RS molecule.c transfor.c abstree.h abstree.c
Added much better support for a wide variety of element
types by introducing element handles. Van der Waals radii
and CPK colours are now maintained for a much larger number
of atom types.
[27/06/93] RS command.c render.c render.h transfor.c transfor.h
Implemented the "ssbond <value>" and "hbond <value>" commands
to represent hydrogen bonds and disulphide bridges as thick
cylinders as well as dashed vectors. Significantly altered
the dynamics of RasMol by making backbone, hbond and ssbond
selection lazy. All these modes always clip vectors and
cylinders. This'll speed up transformation and selection.
[27/06/93] RS rasmol.c raswin.c abstree.c abstree.h
Added predicates for "aliphatic" and "aromatic" predefined
sets. Separated expression handling from molecule.c
[27/06/93] RS command.c graphics.h x11win.c mswin31.c
Added the "hourglass" variable to rasmol, that enables and
disables the use of the hou glass cursor whilst RasMol is
busy drawing and image. This was infuriating during DDE.
[27/06/93] RS render.c pixutils.c
Implemented the section slabmode to draw only a two a cross
section on the current clipping plane. Modified the atom
picking to accept this mode, and fixed a minor bug in the
"half" and "solid" slabmodes for drawing and picking. Removed
clipping code from the shadowing scanline routine.
[24/06/93] RS outfile.c
Corrected problem when outputing postscript files. A rounding
error when shrinking a picture to fit a page resulted in an
axis being scaled by zero. Thanks to Ian Morrison.
[23/06/93] RS !RasMol and RasWin added to the EMBL file server and
anonymous FTP server in Heidelberg, in the directories
/pub/software/dos and /pub/software/unix of
ftp.embl-heidelberg.de
[22/06/93] RS x11win.c
Fixed problem in selecting the required visual class that
caused RasMol to crash when running the OpenWin3 server.
[22/06/93] RS rasmol.h
Added warning messages to the RasMol banner to describe
current visual depth and if not displaying interactively.
[21/06/93] RS molecule.h molecule.c
Added short radius and irad fields to HBond structure
to allow for `thick' hydrogen and disulphide bonds.
[21/06/93] RS pixutils.c command.c render.c outfile.c
Ensured all function prototypes were surrounded by #if
defined(__STDC__) || defined(IBMPC) to avoid errors with
non ANSI C compilers and MS DOS compilers.
[20/06/93] RS Makefile
Added the "-systype bsd43" and "-signed" options to the mips
entry for sysv and bsd43 domains E&S ESV workstations thanks
to Andy Sheppard (mbasd@seqnet.dl.ac.uk)
[18/06/93] RS !RasMol version 2.1 added to the Frequently Asked
Questions (FAQ) list of comp.graphics in the section on
molecular visualization stuff. A RasMol entry ias also
added to the molecular graphics menu of the John Hopkins
University Medical Library Gopher system.
[18/06/93] RS !Announced first public release of RasMol and RasWin
version 2.1, available by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol. The announcement
was made in both bionet.software and comp.graphics newsgroups.