RasTop Manual | Home | All Commands | Notice
Home | About help | Copyrights | License | Installing & using RasTop | Library

ChangeLog History

These logs list all changes made to rasmol source since the release of version 2.1 on the 18th of June 1993 by Roger Sayle.

>     RasTop 2.0x
>     RasTop 2.0
>     RasTop 1.3.1
>     RasTop 1.3
>     RasMol 2.7.1
>     RasMol 2.7.0.1
>     RasMol 2.7.0
>     ChangeLog 9
>     ChangeLog 8
>     ChangeLog 7
>     ChangeLog 6
>     ChangeLog 5
>     ChangeLog 4
>     ChangeLog 3
>     ChangeLog 2
>     ChangeLog 1

### RasTop 2.0x ChangeLog

    [05/05] PV
    	- pixutil.c, repres.c: converted calculations for ribbons to double.
    	- multiple.c: Added SideLen and Offset to VarList.
    	- infile.c: UpdateFeature() Corrected bug responsible for incorrect drawing of
    	  ribbons in protein models. Thanks to Shuji Tomoda for reporting the bug.
    	- command.c, transfor.c: Added jmol command spacefill -<value> to specify
    	  radii in percentage of CPK values.
    	- transfor.c: Put 0.60 factor for LastSpecShade calculation.

    	PV - HB
    	- Added modifications from rasmol 2.7.2.1.1 by HB.

    [04/04] PV
    	- infile.c:ProcessPDBBond() Hacked to allow multiple bonds through CONECT
    	  record to be drawn, but will work only for consecutive identical CONECT
    	  record. This facility disapeared in the rasmol 2.7 series, thanks
    	  to Malcolm Stephen for reporting the problem.
    	- outfile.c: added routine WriteBMP32File() to save bmp file in 32-bits on
    	  windows platform.
    	- command.c:ProcessFile(): Corrected bug with connectivity of xyz files
    	  (Info.bondcount < (MainAtomCount+HetaAtomCount)-Info.chaincount is wrongly
    	  calculated because chaincount equals MainAtomCount in this case. See
    	  correction. Thanks to Filipe Tiago de Oliveira for reporting the problem.
    	- Added menu option to disable automatic running of default Representation
    	  script file upon file loading.

    [03/04] PV
    	- see command.c: attempted to implement the new translate command. The
    	  possible mixing of absolute and relative units makes it very confusing.
    	  We will not deprecate <position> this time!
    	- transfor.c,repres.c/.h: modified restrict command to include Monitors,
    	  dot surface, SS bonds, and H-bonds.
             - Modified reset command: the world scenery is zoomed to fit exactly the
    	  screen with commands "reset world" or "reset" with world on; see ResetAxes()
    	  and getWorldRadius90;
    	- got stupid bug in ZapDatabase() that prevented ReRadius() on closing,
    	  sometimes resulting in molecules not opening at the correct size.

    [02/04] PV
             - Modified zooming effect on scrolling bars from command panel;
    	- Added command <set language default>

    [01/04] PV
    	- Added loading of preferences file located in lib folder;
    	- Added Scripting bar;
    	- Modified Preferences to save all window states.

    [10/03] PV
    	- cmndline.c: Modifid MouseMapping MouseRasMol to allow zooming from center
    	  of screen (pseudo world Z-translation) while pressing the two mouse cliks
    	  in RasMol mapping.
    	- tranfor.c: corrected function Round(), thanks to Audric Schiltknecht.
    	- Change rounding to function Rint().
    	- Corrected bug in InitInstance, thanks to Joachim Strub.

    [01/03] PV
    	- infile.c: Changed coordinate saving in all formats;
    	- script.c: Fixed povray code.

    [10/02] PV
    	- command.c: rewrote save command;

    [09/02] PV
    	- pixutil.c: [UpdateAcross] corrected bug.
    	- infile.c [SavePDBMolecule]: Changed saved coordinates to current coordinate
    	  system - mod suggested by Andrew Horsfield.
    	- multiple.c: Corrected bug (missing ElemDesc in VarList).
    	- prefer.c: Changed rasmolprefs localisation to C:\Document and Settings\userdir\
    	  \rasmolprefs.
    	- Changed internal value of Shapower.
    	- command.c: corrected bug in rotate command.
    	- Removed all direct calls in rasmol core from rastop gui.

    [06/02] PV
    	- render.c [TestAtomProximity]: Corrected bug on ptr - Thanks to Naoum Salem.

    [05/02] PV
    	- colorbar.cpp: changed order of background in ItemList. Suggested by
    	  Naoum Salem.
    	- selectbar.h: corrected carbon selection, error reported by Naoum Salem.
    	- molecule.h: corrected of structure _HBonds col from byte to short; thanks
    	  to Naoum Salem.
    	- commande.c: Corrected error on "save molecule" command and error on
    	  fclose, thanks to Naoum Salem.
    	- command.c [ExecuteTitleCommand]: Corrected bug, thanks to Naoum Salem.
    	- rasdoc.cpp [ManageOpening]: Changed opening script according to extension.
    	- rasdoc.cpp [openfromdoc]: Changed file filter.
    	- rasdoc.cpp [savedmodified]: terminated script case.

    [03/02] PV
    	- rasdoc.cpp, rasview.cpp, rasgraphics.cpp: improved handling of zoom
    	  factor for printing and copying to clipboard.
    	- selecbar.h/,c: Added current selection to selection toolbar, suggestion
    	  from Naoum Salame.
    	- rasgraphics.cpp: Added a refresh in paste selection routine.

    [01/02] PV
    	- repres.c: improved connolly surface drawing;
    	- transfor.c: improved potential surface rendering.

###
RasTop 2.0 ChangeLog

    This log contains changes made from rastop 1.3.1 to rastop 2.0. Numerous
    changes were adapted from rasmol 2.7.2 and 2.7.2.1 from Herbert Bernstein.

    [12/01] PV, all files.
             - Added DepthCue.
             - Doubled colour shades (HICOLOR).
             - "Prepared" rotation, translation, and zoom commands.
             - Added commands "scale","colour axes world","reset worlddepth",
              "show worlddepth", "colour dots none", and "position world".
    	- repres.c: Added code to the Richards-Connolly surface.
    	- Changed management of dot color.

    [10/01] PV
    	- Added command position.
    	- Added help html command.

    [09/01] PV
    	- pixutil.c: Corrected bug in CommonVectStep.
    	- command.c: Corrected zoom command.

    [08/01] PV
    	- transfor.c,script.c: Normalized Range for calculating translation
    	offsets. This changes classical translation scripting (see rastop
            	help).
    	- command.c: Added with corrections the "set stereo"
            	command modification from rasmol 2.7.2.1 by H. Bernstein -
    	see other stereotok as well.
    	- render.c: Inverted left and right image - the last and correct
            	image is now the left one. Adjusted IdentifyAtom function for picking in
            	stereo.
    	- FindDisulphideBridges(): Corrected bug on slist.
    	- molecule.c/.h: Added function ReclaimAllBonds.
    	- transfor.c/.h: Added function PrepareBondRotate.
    	- command.c: Corrected bug on INVERT in rotate bond command.
    	- vector.c: Corrected SubstractAtom.
    	- Replace BondsSelected by RotBondsList.
    	- vector.c: Added function ZeroMatrix.
    	- All: Added triple coordinate system.
    	- All: Improved way to calculate centre rotation.
    	- Command.c: Modified ExecuteShowCommand.
    	- abstree.c: Modified DescribeObj.
    	- Corrected inversion in RotYMatrix.
    	- render.c: Corrected Y axis labeling.
    	- command.c: Added DescribeWorld function.

    [07/01] PV
    	- All project: Fixed Filemodified variable.
    	- Put ShadePower scripting values like in RasMol 2.7.2.1 [H. Bernstein].
    	- command.c: Added ExecuteResetCommand() function.
    	- render.c (DrawFrame) Corrected SlabInten.
    	- (mostly) command.c: Wrote saving and opening of rsm files.
    	- multiple.c: Added with changes function ReRadius() from rasmol
            	2.7.2.1.
    	- transfor.c: Modified InitialTransform to adjust zoom factor upon
            	loading.
    	- render.c: Modifid ResizeScreen function.
    	- transfer.c: Modified DrawWorld() to prevent conflict with maxzoom
            	during cliboard manipulations.
    	- script.c: Added macro IsZero(x).
    	- All: variable RefreshState: Found deep conflict between refreshing,
            	saving,and fast drawing. Modifications may not be ok in 8-bit mode
    	(ColourMap).
    	- Added corrections from rasmol 2.7.2.1 by Herbert Bernstein:
    	- molecule.c: SimpleAtomType(), ComplexSimpleAtomType(): Corrected
            	bug with ElemnDesc.

    [14/04/01] HJB script.c
    	Correct error in writing scripts with partial use of spacefill.
    	Thanks to Steven Vik <svik@mail.smu.edu> for reporting the
            	problem.

    [02/04/01] HJB abstree.c, abstree.h
    	Increase space for atom names from 4 to 12 characters.

    [02/04/01] HJB infile.c
    	Increase limit on atom names for CIF from 4 to 12 characters.

    [02/04/01] HJB several
    	Make dial indices symbolic (PV: Not fully done yet!)

    [21/08/00] HJB command.h
    	Add space after "__huge"

    [23/02/00] HJB infile.c
    	Fix *- for - typo in XYZ and MOL2 input of coordinates

    [05/01] PV
    	- Clipping is not reset anymore upon "reset" in order to
            	respect the world construction when new molecules are loaded.
    	The old way of bringing clips to the center of the molecule
    	does not seem logical.
    	- Added command "reset ligth", "reset slab", and "reset depth".
    	- Added commands "refresh off" and "refresh on".
    	- Cmndline.c: Added function ProcessWheelDial().
    	- ResizeScreen: Corrected background redrawing in Displaymode.
    	- DefineColourMap: Darkened DisplayMode Background.
    	- Added variable SRange and fixed stereo mode.
    	- Finished code for slab and back-clipping (all files). Added code
    	for commands "slab world <number>" and "slab world origin",
    	and equivalent for depth mode.
    	- Finished code for manipulation of rotation centers; made
    	center visible in display mode; added centre command syntax
    	from rasmol 2.7.2.1.
    	- Added commands:
    	"centre world": Translate world origin to centre of screen,
            	world is translated at the same time;
    	"centre origin": Bring center to world origin
    	"centre origin centre": Translate world origin to actual
            	rotation center; this is a "world" destructive command!

    [04/01] PV
    	- Added new panes to status bar.
    	- command.c: errorcount versus rastop 1.3.1, corrected bug in
    	executecommand.
    	- Corrected ExecuteTitleCommand() and SetTitle() for new titles.
    	- Changed edit menu; put accelerator key to "enter rasmol
            	command".
    	- Modified command panel, added world button.
    	- Modified DisplayMode.
    	- Added commands "molecule hide" and "molecule Sow" (see comdline
    	and pickatoms + all molset->visible references).
    	- DisplayRibbons(): Corrected alignement of DNA helix.

    [03/01] PV
    	- Added fast drawing (variable FastDraw).
    	- Added variable DrawWorldAxes.

    [02/01] PV
    	- Added variables WAxe[], Zo[], ZRange, and DRange.
    	- transfor.c: Added functions PrepareWorldTransform(), ResetWorldAxes.
    	- vector.c/.h: Added function CopyMatrix3(), IdentityMatrix3().
    	- Adjusted ReSizeScreen() code.
    	- Added zoom to comndline.c in rotate all mode; Corrected a few
    	bugs in ProcessMouseMove().
    	- Introduced molecule offsets MOffset[] to position molecules during
    	all transformations; X/Y/ZOffset are equivalent integers used
    	for calculating rendering.
    	- Changed DialValue for translation to modulo[2] (free translation).

    [01/01] PV
    	- Added code for preferences.
    	- Added code for default script in default representation.
    	- rasview.cpp rasdoc.cpp: Corrected Windows 2000 bug.
    	- Passed conditions on RegisterAlloc() into the function.
    	- Added bond rotation code, renamed wbrotate.c brotate.c (all the
    	world-rotate code is tranfered into transfor.c).
    	Added ChangeBondOrder(), removed NewBond, removed RotBond mode, and
    	added PickRBond picking mode.
    	Added command "bond <number> <number>
            	single/double/triple/unbound".
    	Added command "set picking bond rotate" and "set
            	picking rotate bond".
    	Removed function RemoveBond(); Attempted to correct erroneous hbond
    	and ssbond in BondRotate() by simply destroying bond lists!
    	- Added code for picking lightsource in picking mode.
    	- Added PickLight mode;
    	- Added F1 help.
    	- Added new icons in toolbar.
    	- Adjusted WriteScriptFile();
    	- Modified WriteScriptDots();
    	- Renamed DeleteSurface() DeleteDotSurface();
    	- Renamed CalculateSurface() CalculateDotSurface();
    	- Added function WriteScriptSurface() in script.c;
    	- Corrected bug in WriteScriptAtomSets().

    [12/00] PV
    	- Removed ProcessDoc() function; added ResetUserBox().
    	- rasview.c cmndline.c/.h SetPickMode()
    	Added code for cursor mode.
    	- command.c transfor.c molecule.h (and others)
    	Added PreviousTok and code for saving previous selection.
    	Added flag2 for RAtom (flag is full).
    	- command.c rasdoc.c/.h rastop.c multiple.c (and others)
    	Added code for handling rsm files by rasmol;
    	Added ErrorCount and ErrorFlag to handle wrong scriptfiles.
    	- graphic.h SetCanvasTitle() SetTitle() ExecuteTitleCommand()
    	SelectMolecule(): changed title code.
    	- All: Removed (rastop) variable MoleculeFileName.
    	Put "strcpy(Info.filename,DataFileName);" uniquely in
            	ProcessFile()with correction for "inline" files in DivertoData().
    	- Transfered new 2.7.2 FetchFile function to ProcessFile()
    	- Confusion on attribution of DataFileFormat. Only attribution in
    	processfile() is conserved.
    	- DrawFrameOne() transfor.h: Replaced ApplyTransform() by
    	ApplyTransformOne().

    [11/00] PV
    	- multiple.c command.c
    	Transfered ZapDatabase() into multiple.c; changed name to Zapmolecule();
    	created new Zapdatabase() for zapping all molecules. Added command
    	"zap molecule", "zap selected" and "zap all" with "zap" synonymous of
    	"zap all".
    	- WriteVRMLWireframe(): typing bug corrected.
    	- transfor.c/.h wbrotate.c/.h: Transfered WorldRotate to Transfor.c
    	- All: Added rasmol 2.7.2 code for multiple molecules
    	- IdentifyAtom(): Corrected bug with UseDepthPlane
    	- transfor.c: Changed carbon cpk color to white when no hydrogen.
    	Changed default cartoonheight.

    [10/00] PV
    	- pixutil.h/c rastop.cpp
    	Changed cylinder code. Added code to draw cylinders with flat cap.
    	Code still needs some fixings.
    	- pixutil.h/c repres.c
    	Completed cartoons code.
    	- rasview.cpp rasdoc.cpp mainframe.cpp pannel.h/.cpp
    	Reorganized automode.
    	- LightX, LightY, LightZ, LightLength, ColConst, DefaultTok,
    	LightsourceTok, HeadlightTok
    	Added multidirectional lightsource.
    	- command.c
    	Corrected bug in parsing of shadepower command.
    	- render.c repress.c pixutil.c
    	Fixed use of InvertY with LightDot and switched to ORIGINAL lighting.

### RasTop1.3.1 ChangeLog

    This log summarizes changes from RasTop version 1.3 to RasTop version 1.3.1

    [03/01] PV

    - mainframe: Changed font generation;
            changed selectbar initialization.
            - Added profile "Selection" for the select bar.
            - render.c/IdentifyAtom(): Made atoms behind the depth plane not
            identified.
              (thanks to Ian Gibbons for reporting the bug and other
            suggestions)
            - command.c: Added ErrorCount, ErrorFlag and MAXERROR.
            - mainframe: Removed function OnDropFile to allow dropping of pdb files.
            - rasview/rasdoc: Added macro STOPTIMER and STARTTIMER
            - pannel.ccp/h: Changed auto by spin. Made variable m_autostatus
            private.
            - Changed two icons in the resources.
            - transfor.c: Changed carbon cpk color to white when no hydrogen.
            - script.c: Corrected output error in WriteAtomSelection.
            - command.c: Corrected bug in parsing of shadepower command.
            - script.c: Added exittok at the end of saved script.
            - rasview/rasdoc: Corrected bug in drawing and removed unuseful code.
            - repres.c: Corrected drawing of ribbons at large zoom.
            - render.c/displayboxes: Corrected bug on axe position when moving
            center.
            - transfor.h: Removed duplicated variables
            - SetPickMode, CentreTranform: Changed RedrawFlag.
            - Switch Help command to mainframe and activate help on F1

### RasTop1.3 ChangeLog

    Consult also RasMol changeLog and RasMol2.7.1 changeLog.

    This log contains all changes made to RasMol
            source independently of RasTop. Initial work was done on version 2.6.4,
            but was quickly updated to the newer version 2.7.1 by Herbert Beirnstein.

    [21/09/99] PV command.c
            Changed output for one-letter-code sequence in series of 50
            characters with a space each subgroup of 10.

    [21/09/99] PV command.c (ExecuteCommand())
            Added command "trace dots <value>" allowing trace dots
            representations of varied radii.

    [21/09/99] PV command.c / render.h /
            render.c / transfor.h .c
            Added four new picking modes:
            - select an atom: PickAtome
            - select a group: PickGroup
            - select a chain: PickChain
            - modify bonding/add multiple bonds: PickBond
            Allowed picking parameter shift = -1 when Ctrl key is down to deselect
            an atom (a group, a chain) from the current selection.

    [21/09/99] PV cmndline.c (ProcessCharacter())
            Added <Esc> character to interupt script pausing.

    [21/09/99] PV pixutils.c
            Set ARCSIZE to 32768 under MSWIN, allowing drawing cylinders with
            radii up to 250 RasMol Units. Current implementation gives a maximum
            of 75 RU at maximum zooming. Mac implementation should be verified.

    [21/09/99] PV script.c
            Completed scripting for "trace dots <value>", backfade,
            shadow,and stereo.

    [21/09/99] PV
            Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
            - declared InterruptPauseCommand() and ResumePauseCommand()
              in command.h
            - declared TestDisulphideBridge() in molecule.h
            - explicited all conversions long to short in infile.c /*casting*/
            - excluded all unreferenced variables in infile.c /*unreferenced*/
            - included graphics.h in molecule.c
            - fixed casting in drawstar() and clipstar() in pixutils.c
            - declared DefineShade() in transfor header
            - fixed casting and referencing in script.c
            - declared LoadDotsFile() in repres header
            - declared SetFontStroke() in pixutil header
            - missing WritePOVRay3File() declaration in script header
            - declared cif_free_handle() in cif header
            - missing declaration of cif_parse in cif.h

    [22/09/99] PV repres.c
            Fixed bug in DisplayRibbon() that produced cartoon like structure in
            ribbons covering only parts of chains or mixing ribbon types.

    [22/09/99] PV abstree.h .c
            Fisrt step for saving atomsets & identifiers in RasMol scripts (SetSize
            to 100 and SymEntry and SymbolTable in header).

    [22/09/99] PV repres.h command.c
            Improved label picking mode (LabelFormat to store the current label
            string,the command "label {<string>}" is disabled in
            picking mode but save the format).

    [24/09/99] PV cmndline.c
            Correlated mouse binding to global variable MouseMode;
            Removed EnableMenus(state==1) in ResetCommandLine();
            Fixed mouse binding with INVERT on y values;
            Fixed bug on capture status on mouse-up;
            Added MM_PREV to mouse binding for deselection;
            Fixed INVERT on y value for mouseup!

    [28/09/99] PV transfor.c
            Fixed bug (?) with stars, making them mutually exclusive with spheres.
            Adjusted bondmode in EnableWireframe().

    [29/09/99] PV molecule.c
            Fixed bug in FindCisBonds() (no zeroing of last group cisbondflag);
            Added ability to convert triple bond to single (CreateBondOrder())

    [01/10/99] PV command.c
            Fixed initialization SeqFormat and CalcBondsFlag (ExecuteConnectCommand);
            Fixed bug in coloring strands (missing strandtok).

    [07/10/99] PV command.c abstree.c script.c render.c
            Changed coordinates and phipsi output, modified output for showcommand;
            Adjusted threshold in DisplaySelected.

    [07/10/99] PV cif.c
            Fixed memory allocation bug (VisualC++?) in cif_make_handle;

    [07/14/99] PV abstree.c transfor.c
            Added shortcuts for direct evaluations of atomsets (BuildAtomSet(),
            SelectZoneExpr()); gain up to 15 seconds of computer time on very
            large molecules.
            Added variable ModelInclude to select either in one model or in all
            models;

    [17/10/99] PV command.c
            Modified CommandError output (shortened file name).

    [19/10/99] PV
            Release RasTop1.1

    -------------------------------------------------------------------------

    [20/10/99] PV script.c
            Added temporary output on command line when null file in WriteScriptFile,
            which edits a rasmol header file.

    [22/10/99] PV command.c transform.c .h
            Added function ReadAtomSelection() which escapes the parser under
            the form:"select (< or >) x1[-x2],...,xi[-x(i+1)](> or <)"
            where '<' starts or continues an atom selection, '>' continues or stops
            the current selection, - indicates a bloc of consecutive atoms, and xi
            are atomnos. Required DisplaySelectCount() to be global.

    [27/10/99] PV command.c script.c .h graphics.h
            Added function WriteAtomSelection() and WriteScriptPosition();
            Added commands "clipboard selected", "clipboard
            position" "clipboard
            image" and "clipboard paste" and corresponding functions:
            ClipboardImage( )
            ClipboardPosition( )
            ClipboardSelection( )
            ClipboardPaste( )

    [29/10/99] PV command.c script.c .h graphics.h
            Added function WriteScriptAtomSets() to write atom sets to the script.

    [02/11/99] PV repres.h transfor.h
            Added variables DotR,DotG,DotB,DotDensity, and UseDotColPot for
            saving dot characteristics.

    [09/11/99] PV command.h/.c
            Added MoleculeFileName variable and SaveRsmMolecule() function;
            Modified save command to address "save <filename>" to
            SaveRsmMolecule().

    [09/11/99] PV rasmol.h command.c

            Added ProcessDoc and SaveDoc functions which allows add-ons (like
            RasTop)to react to newly loaded molecules, zapping, and saving of
            molecular data.

    [22/11/99] PV molecule.c script.c
            Modified CreateNewBond() to prevent pdb files without atom description;
            Adjusted ProcessFile() and FetchFile() to allow attribution
            of DataFileFormat when no Database is created.
            Modified output of WriteScriptHBonds();

    [12/08/99] PV command.c
            ResumePauseCommand( ), added '\r' to terminate curline (bug? resulted in
            non opening of subscripts when LF/CR in the script file).

    [12/08/99] PV rasmol.h command.c
            Added function RefreshView() in rasmol.h to replace RefreshScreen() in
            command.c to allow refreshscreeen from inside RasMol.

    [12/09/99] PV command.c
            Added Beginwait/endwait in ProcessFile().

    [12/10/99] PV command.c token.c
            Added CopyTok for "copy" command equivalent to
            "clipboard" and shorcut for "paste" command.
            Added SELECTION as an homonymous keyword to SELECTED

    -------------------------------------------------------------------------

    Started version 1.3.

    [12/14/99] PV transform.c and others
            Added function CentreTransform() to either move the origin in the molecule
            or move the molecule to the origin (origin = True ). Added variables
            Cenx,y,z, which mesure distance centre-origin. Changed DrawTwinVector to
            ClipTwinVector in DisplayWireFrame() (render.c).

    [12/14/99] PV
            Added variables ShiftS and UseAutoDepthCue that adjust DepthCue
            with slabbing.

    [12/17/99] PV render.c
            Added centre correction in DisplayBoxes().

    [12/18/99] PV
            Added code for backclipping based on ZOffset. New variable UseDepthPlane
            and DialValue[8].

    [12/20/99] PV script.c
            Added more precision to rotate, translate, zoom, and slab commands in
            WriteScriptFile() and WriteScriptPosition(). This is important
            for passing cliboard content and saving centre. Fixed centre scripting.

    [01/03/00] PV transfor.c
            Fixed bug (and modified) function Power() to handle Specpower.

    [01/14/00] PV molecule.c
            Set Info.filename as alternative title.

    [01/16/00] PV transfor.h/.c token.h/.c script.c
            Added ShadePower in DefineColourMap(), which brings some interesting
            shade variations. Added ShadePowerTok and command "set shade x" with
            x between -20 to 20.

    [01/16/00] PV cmndline.c PerformMouseFunc()
            Corrected MM_CLIP to access clipping with the mouse;
            Added MM_DEPT to access backclipping (depth) with the mouse.

    [01/16/00] PV
            Completed 32-bits version. Code a bit messy, especially for
            clipboard and background operations. Will probably not compile on
            other compilers. bmp file saving not done in 32 bits.
            Added code for command "set dot <value>" which adjusts
            the size of the dots in a rather rough way.

    [01/17/00] PV script.c
            Corrected bug in WriteScriptAtoms().

    [01/17/00] PV render.c
            Solved problem in regenerating background in 32 bits in ReSizeScreen().

    [01/17/00] PV command.c ExecutePauseCommand()
            Added a RFRefresh for refreshing RasTop screen.

    [01/28/00] PV render.c ResetRender()
            (Bug?) Finally found old problem with shadows in RasTop. Missing
            a ResetVoxelData() on zapping. This is a potential source of problems
            when successively opening scripts containing shadows in RasMol.

    [01/30/00] PV command.c
            Added command "select view" and corresponding code, which allows to
            select a part of a molecule based on screen display.

    [01/31/00] PV command.c
            Added code for selecting atom areas with mouse:
            - changed PickAtom() function name in PickAtoms();
            - changed PicAtome identifier in PickAtom;
            - added function SelectArea() and DisplayArea();
            - added code for command "select view";

    [02/02/00] PV pixutil.c render.c
            Added function ClipDashLine();
            Changed display of cells with dashed lines in DisplayBoxes().

    [06/01/00] PV
            Finish help; Release version 1.3

### RasMol 2.7.1 ChangeLog

### Changes from RasMol 2.7.0.1 to create RasMol 2.7.1:

    [15/07/99]	HJB	documentation
    		Add Dunix binaries.  Thanks to David Atkinson

    [06/07/99]	HJB	all
    		Release 2.7.1

    [05/07/99]	HJB	documentation
    		Cut-off date for Release 2.7.1 documentation changes.

    [22/06/99]	HJB	all source
    		Cut-off date for Release 2.7.1 code changes.

    [22/06/99]	HJB	command.c
    		Save fact that a data file was loaded inline.  Add
    		processing for star command, all new options for
    		bondmode [all | none | not bonded ]

    [22/06/99]	HJB	infile.c
    		Update DataFileFormat after autorecognition.

    [22/06/99]	HJB	molecule.h
    		Add MarkAtoms to hold new bondmode flags.

    [22/06/99]	HJB	pixutils.c, render.c
    		Add code for new star command.

    [22/06/99]	HJB	script.c
    		Add logic to write star command output.  Report data
    		loaded as CIF or as inline correctly.  Warn users
    		that inline data is not being written out.  Check
    		inversion of Y-axis on POVRAY3.  Thanks to Curt
    		Haltiwanger for suggesting marking non-bonded atoms
    		on wireframe displays.

    [22/06/99]	HJB	transfor.c
    		Add code for new star command, new bondmode options.

    [18/06/99]	HJB	pixutils.h, pixutils.c
    		Change name of DisplayString to DisplayRasString to
    		avoid a conflict with X libraries.  Add FontWid array
    		to hold character widths (FontSize for FS, FontSize/4
    		+1 + maximum x position for PS).  Add FontStroke logic to
    		write cylinders instead of lines when FontStroke is not
    		zero.

    [18/06/99]	HJB	render.c
    		Change name of DisplayString to DisplayRasString to
    		avoid a conflict with X libraries.

    [18/06/99]	HJB	repres.c
    		When FonstStroke is non-zero, don't offset character
    		color by (ColourMask>>1), to allow room for color
    		adjustments in cylinder drawing.

    [18/06/99]	HJB	script.c
    		Add logic to write PS flag for proportional spacing
    		on set fontsize, and logic to write set fontstroke n.

    [18/06/99]	HJB	tokens.c, tokens.h
    		Add tokens for BlueTint (BlueTintTok), Brown (BrownTok),
    		FontStroke (FontStrokeTok), FS (FSTok), Gold (GoldTok),
    		Gray or Grey (GrayTok), GreenTint (GreenTintTok), HotPink
    		(HotPinkTok), Pick as an alternative for Picking
    		(PickingTok), Pink (PinkTok), PinkTint (PinktintTok),
    		SeaGreen (SeaGreenTok), SkyBlue (SlyBlueTok),
    		YellowTint (YellowTintTok)

    [13/06/99]	HJB	command.c
    		Change processing of load inline command to work from
                    the currently opened script, saving the file position.
                    Accept HEADER and DATA_... as commands in a script,
                    processing that line and all subsequent lines as a
                    data file, unless a prior load inline command was already
                    done

    [12/06/99]	HJB	infile.c
    		When processing a PDB file, test for DATA_... until
                    a non-comment, non-blank line is found.  Revert
                    to CIF processing if DATA_... is found.

    [11/06/99]	HJB	infile.c
    		In PDB format input extract EXPDTA for Info.technique.
    		In CIF format input accept _audit_block_code for the
    		entry ID, _exptl.method, _diffrn_radiation.probe or
    		_diffrn_radiation_probe for Info.technique.  Preserve
    		low order bits of coordinates in xtrl, yrtl, ztrl.  On
    		PDB output, report Info.technique in EXPDTA and reinsert
    		low-order bits for coordinates.

    [10/06/99]	HJB	abstree.c
    		Add code to report coordinates for show selected cordinates

    [10/06/99]	HJB	command.c
    		Recognize new commands, picking coordinates,
                    show selected cordinates.  Update default title produced
    		by title command.

    [10/06/99]	HJB	molecule.h
    		Add new Info fields for date and technique.  Extend
    		identcode to 80 columns.  Add CRD to Selection enum type.
    		Add prototype for ReviseTitle.

    [10/06/99]	HJB	render.h, render.c
    		Add code to report coordinates for picking coordinates,
    		define PickCoord symbol.

    [10/06/99]	HJB	tokens.h, tokens.c
    		Add code recognize COORD, COORDS, COORDINATE, COORDINATES for
    		new CoordTok, DATA_... for CIFDataTok, HEADER for HeaderTok

    [09/06/99]	HJB	molecule.c
    		Put PDB entry ID and EXPDTA info into canvas title, report
    		EXPDTA data from Info.technique on reading file.

    [06/06/99]	HJB	infile.c
    		Restore the origin on PDB and other outputs.

    [06/06/99]	HJB	script.c
    		Change script output to include centering and
    		change various coordinate outputs to restore
    		origins the z-axis orientation.

    [06/06/99]	HJB	command.c
    		Add command centre [CenX,CenY,CenZ] to center by offsets
    		from centre of gravity.

    [03/06/99]	HJB	render.c
    		Remove call to TranslateToCentre, hold centering
    		in CenX, CenY and CenZ, decoupled from dials,
    		add RFRotate to ReDrawFlag on centering.  Thanks to
    		Bohdan Schneider for pointing out the problems with
    		centering.

    [03/06/99]	HJB	transfor.c
    		Remove TranslateToCentre, remove processing of CenX,
    		CenY and CenZ from dial values, and put it into
    		computation of ptr->x,y,z

### Changes after release of RasMol_2.7.0.1:

    [27/04/99]	HJB	README.html, Changelog.html, INSTALL.html, manual
    		Add navigation links at top and bottom of each page.
    		Add links for gzipped versions of raswin.hlp, rasmol.hlp.
    		Thanks to E. Martz and Kjeld Olesen.

    [27/04/99]	HJB	INSTALL.html, manual
    		Replace empty copy of INSTALL.html in doc/, correct
    		embedded html in manual.  Thanks to Kurt Giles.

### RasMol 2.7.0.1 ChangeLog

### Changes from RasMol_2.7.0 to create RasMol_2.7.0.1:

    [22/04/99]	HJB
    		Announce RasMol 2.7.0.1 on pdb-l@rcsb.org,
    		rasmol@lists.umass.edu, mmciflist@ndbdev.rutgers.edu

    [11/04/99]	HJB	*.c, *.h
    		Update all comment blocks for new version and date

    [11/04/99]	HJB	abstree.h
    		Realign Pred... to agree with ...Tok to correct
    		misaligned introduced by HJB (not AM) during merge of 2.6x1
    		into 2.7.0.

    [11/04/99]	HJB	tokens.h
    		Fix definition of IsPredTok

    [09/04/99]	HJB	molecule,h
    		Make residue identification case-insensitive.

### RasMol 2.7.0 ChangeLog

### Changes from RasMol_2.6.4, RasMol2.6x1 and RasMol_2.6_CIF.2 to create RasMol_2.7.0:

    [30/03/99]	HJB	all
    		Cleanup and release of version 2.7.0

    [23/03/99]	HJB	abstree.c
    		Add code to select on alternate conformers.  Increase
    		accuracy of torsion angle calculation.

    [23/03/99]	HJB	command.c, command.h
    		Make InitHelpFile generally available, change to
    		WriteString for reporting CisBondCutOff for use on mac,
    		report models on show selected.

    [23/03/99]	HJB	rasmol.c, raswin.c, rasmac.c
    		Add suggestion for help notice to initial text lines.

    [23/03/99]	HJB	script.c
    		In order to support mac introduce WriteBuffer and
    		change all fprintf(outFile, ... to WriteBuffer, provide
    		code from fisipl for Ramachandran printer plot.  Handle
    		signs of torsion angles.  Thanks to F. C. Bernstein.

    [23/03/99]	HJB	tokens.h, tokens.c
    		Add RamPrintTok, RPP, RDF, etc., hook POVRAY3 to the
    		new POVray code.

    [20/03/99]	HJB	*.h, *.c
    		In general, the RasMol_2.6_CIF.2 version was used as a base
    		and upgraded with the RasMol_2.6.4 changes.  The exceptions
    		are below

    [20/03/99]	HJB	infile.c
    		Cell parameters are read with the double routine ReadDecValue
    		from 2.6_CIF.2, rather than ReadValue2 from 2.6.4

### Changes from RasMol_2.6 to create RasMol_2.6x1:

    [15/2/98]	AM	abstree.c, abstree.h
    		Add PredCisBond, DescribeObj, CalcPhiAngle, CalcPsiAngle,
    		CalcOmegaAngle, shift torsion angle calculations 180
    		degrees.

    [15/2/98]	AM	command.c
    		Add FindCisBonds, CisBondCutOff, show of selected chains,
    		groups, atoms, show and write of phi-psi angles

    [15/2/98]	AM	molecule.h, molecule.c
    		Add CIS bond logic

    [15/2/98]	AM	rasmol.h, rasmol.c
    		Add USE_FD_SET_TYPE option

    [15/2/98]	AM	script.h, script.c
    		Add WritePhiPsiAngles, code for POV-Ray version 3

    [15/2/98]	AM	tokens.h
    		Add CisBondedTok, RamachanTok, CisAngleTok, PhiPsiTok,
    		define PHIPSI, CISANGLE, RAMACHAN, CISBONDED

### Changes from RasMol_2.6 to create RasMol_2.6.4:

    [8/2/99]	RS	command.c, rasmol.c, scripts.c, rastxt.c, raswin.c
    		rasmac.c
    		Final fixup and release of version 2.6.4

    [27/12/98]	RS	*.h, *.c
    		Remove all non-ANSI-C prototypes and ensure use of ( void )
    		for empty argument lists.  Upgrade all procedure delcarations.
    		Convert to use of MSWIN.

    [27/12/98]	RS	abstree.c
    		Redo torsion angel calculation.

    [27/12/98]	RS	applemac.c
    		Convert to Apple's new routine names

    [27/12/98]	RS	cmndline.c, cmndline.h
    		New routine for mouse, keyboard, dials

    [27/12/98]	RS	command.c, command.h
    		Move routines for mouse, keyboard, dials to cmndline.c.
    		Redo ParseColour.  Reorganize command parsing

    [27/12/98]	RS	infile.c
    		Change references to MMIO to MMIOLIB.  Pass fp and buffer
    		to FetchRecord as argument.  Add ReadValue2, ProcessPDBBond,
    		ProcessPDBUnitCell.  Fix recognition of END. Use
    		InvalidateCmndline and UnusedArgument.  Write MODEL and
    		ENDMDL records when appropriate

    [27/12/98]	RS	molecule.c
    		Reorganize FindResNo as a character-oriented search tree
    		Add Cache.

    [27/12/98]	RS	rasmac.c
    		Convert to Apple's new routine names

    [27/12/98]	RS	rastxt.c
    		New text-only main program

    [27/12/98]	RS	repres.c
    		Add LabelTermnii

    [27/12/98]	RS	tranfor.c
    		Add TranslateToCentre

    [27/12/98]	RS	transfor.h
    		Reorganize the logic defining DefaultAmbient, making
    		the default value 0.4 instead of 0.6, except for E&S, which
    		is still .05.

    [27/12/98]	RS	tokens.c
    		New routine for character-oriented search tree for tokens.

    [01/08/97]	RS	infile.c
    		Decreased the maximum valid alpha carbon to alpha carbon
    		distance to 4.2 Angstroms from 7.0 Angstroms.  Thanks to
    		Kostas Sfyrakis and Harren Jhoti.

    [15/04/97]	RS	molecule.c repres.c
    		Fixed a bizarre feature in the OpenVMS compiler that complained
    		about "a=*b" as "=*" operator is an obsoltete form and may not
    		be portable.  Special thanks to Remington Stone.

    [28/11/96]	RS	rasmol.h rasmol.c
    		Several minor fixes to compile RasMol under VMS.  Special
    		thanks to Adam Ralph (and CCP4).

### Changes from RasMol_2.6_CIF(Rev 1) to create RasMol_2.6_CIF(Rev 2):

    [24/2/99]	HJB	Release of RasMol_2.6_CIF(Rev 2) at
    		http://www/bernstein-plus-sons.com/software/rasmol
    		and announce to mailing lists.

    [21/2/99]	HJB	cif.h
    		Add prototypes of cif_make_handle, cif_read_file,
    		cif_make_file, cif_save_character to avoid compiler warnings

    [21/2/99]	HJB	cif_ctonum.c
    		Remove unneeded values.h

    [21/2/99]	HJB	cif_ctonum.h
    		Correct prototype

    [21/2/99]	HJB	infile.c
    		Add cif_ctonum.h, define LoadCIFMolecule prototype,
    		initialize ch, add return  to avoid compiler warnings.

    [21/2/99]	HJB	abstree.c, cif.c, cif_ctonum.c, command.c,
    		infile.c, molecule.c
    		Use string_case.h instead of  for IBMPC,
    		VMS and APPLEMAC.

    [21/2/99]	HJB	rasmol.h
    		Update version, add some definitions from R. Sayle's
    		2.6.4 in preparation for 2.7.0.

    [21/2/99]	HJB	rasmac.c, rasmol.c, raswin.c
    		Update reported date on startup.

    [21/2/99]	HJB	render.c
    		Add cif_fract.h to avoid compiler warnings.

    [21/2/99]	HJB	string_case.c
    		Replace garbled version, provide string_case.h.

    [21/2/99]	HJB	script.c
    		Initialize first, last, radius, to avoid compiler warnings

    [21/2/99]	HJB	transfor.c
    		Initialize min and max to avoid compiler warnings.

    [10/1/99]	HJB	Release of RasMol_2.6_CIF(Rev 1) at
    		http://www.bernstein-plus-sons.com/software/rasmol
    		and announce to mmCIF mailing list.

    [9/1/99]	HJB	cif.c
    		Change toupper calls to ToUpper calls.

    [8/1/99]	HJB	command.c
    		Add argument to CreateMoleculeBonds to force zapping
    		on connect.

    [8/1/99]	HJB	infile.c
    		Log requested bonds which cannot be made in NullBonds
    		and report to users, add RightJustify to right-justify
    		residue names, recognize _atom_site_disorder_group
    		for small molecule alternate conformerse, recognize bonds
    		which don't have either atom names or atom numbers.

    [8/1/99]	HJB	molecule.c
    		Add argument to CreateMoleculeBonds to force zapping
    		on connect.

    [8/1/99]	HJB	molecule.h
    		Add argument to CreateMoleculeBonds to force zapping
    		on connect, add NullBonds to log requested bonds which
    		cannot be made.

    [8/1/99]	HJB	mswin31.c
    		Use VERSION to construct window title.

    [8/1/99]	HJB	outfile.c
    		Use VERSION to construct Postscript output file header.

    [8/1/99]	HJB	rasmac.c
    		Use VERSION to report version on startup.

    [8/1/99]	HJB	rasmol.c
    		Use VERSION to report version on startup.

    [8/1/99]	HJB	raswin.c
    		Use VERSION to report version on startup.

    [8/1/99]	HJB	script.c
    		Use VERSION to construct various output file headers.

    [8/1/99]	HJB	x11win.c
    		Use VERSION to construct window title.

### Changes from RasMol_2.6 to create RasMol_2.6_CIF:

    [22/12/98]	HJB	Preliminary release of RasMol_2.6_CIF at
    		http://www.bernstein-plus-sons.com/software/rasmol

    [19/12/98]	HJB	command.c
    		correct handling of internal help files under windows,
    		and allow for unix help files on a mac.

    [18/12/98]	HJB	Makefile.in, Imakefile
    		Update for CIF support.

    [09/12/98]	HJB	infile.c
    		Cummulative changes for fractional coordinates,
    		CIF.

    [09/12/98]	HJB	command.c
    		Changes for alt, model labels, colour schemes,
    		CIF.

    [09/12/98]	HJB	molecule.h
    		Cummulative changes for fractional coordinates,
    		new colour schemes, CIF.

    [09/12/98]	HJB	molecule.c
    		Cummulative changes for fractional coordinates,
    		new colour schemes, CIF.
    [09/12/98]	HJB	x11win.c
    		Update comments, menus and version text.

    [09/12/98]	HJB	mswin31.c
    		Update comments, output file commentary.

    [09/12/98]	HJB	outfile.c
    		Update comments, output file commentary.

    [09/12/98]	HJB	script.c
    		Update comments, output file commentary.

    [09/12/98]	HJB	rasmol.c
    		Update comments, output file commentary.

    [04/12/98]	HJB	pixutils.c
    		Update comments, code to stripe bonds for alternate
    		conformers.

    [04/12/98]	HJB	pixutils.h
    		Update comments, protytpes to stripe bonds for alternate
    		conformers.

    [04/12/98]	HJB	rasmac.c
    		Update comments, adjust code for current Metrowerks
    		compiler.

    [04/12/98]	HJB	raswin.c
    		Update comments, adjust code for current Metrowerks
    		compiler.

    [04/12/98]	HJB	tokens.h
    		Update comments, tokens for alt, model colours.

    [04/12/98]	HJB	transfor.c
    		Update comments, add code for alt, model colours.

    [04/12/98]	HJB	transfor.h
    		Update comments, prototypes for alt, model colours.

    [23/11/98]	HJB	abstree.c
    		Add code for %A, %M specifiers, divide u/l case.

    [22/11/98]	HJB	cif_fract.c
    		New routine, derived from cif2pdb by H.J. Bernstein
    		and F. C. Bernstein.

    [22/11/98]	HJB	cif_fract.h.
    		New header for cif_fact.c.

    [22/11/98]	HJB	cif_stx.c
    		New routine, derived from P. Ellis CBFlib parser.

    [23/11/98]	HJB	render.c
    		Update comments, add code to stripe bonds for alternate
    		conformers.

    [23/11/98]	HJB	repres.c
    		Update comments, add code to stripe bonds for alternate
    		conformers.

    [09/09/98]	HJB	cif_ctonum.c
    		New routine, derived from ciftbx by S. R. Hall
    		and H. J. Bernstein.

    [09/09/98]	HJB	cif_ctonum.h
    		New header for cif_ctonum.c.

    [18/08/98]	HJB	cif.h
    		New header for cif.c, derived from CBFlib by P. Ellis
    		and H. J. Bernstein.

    [18/08/98]	HJB	cif.c
    		New routine derived from CBFlib by P. Ellis and
    		H. J. Bernstein.

    [14/08/98]	HJB	rasmol.c
    		Added hooks for termio for Linux.  These changes
    		are similar to, but not identical to the FreeBSD hooks.
    		See the linux conditionals. -- H. J. Bernstein

RasTop Help Site - home | notice | copyright