|Arne Mueller||RasMol 2.6x1 May 1998||© Arne Mueller 1998|
|Gary Grossman and|
|RasMol 2.5-ucb November 1995|
RasMol 2.6-ucb November 1996
|© UC Regents/ModularCHEM|
Consortium 1995, 1996
|Philippe Valadon||RasTop 1.3 August 2000||© Philippe Valadon 2000|
|Herbert J. Bernstein||RasMol 2.7.0 March 1999|
RasMol 2.7.1 June 1999
RasMol 184.108.40.206 January 2001
RasMol 2.7.2 August 2000
RasMol 220.127.116.11 April 2001
RasMol 18.104.22.168.1 January 2004
RasMol 2.7.3 February 2005
RasMol 22.214.171.124 Apr 06
RasMol 2.7.4 Nov 07
RasMol 126.96.36.199 Jan 08
RasMol 188.8.131.52 Mar 08
|© Herbert J. Bernstein 1998-2008|
This version is based directly on RasMol 184.108.40.206, RasMol 2.7.3, RasMol 220.127.116.11.1 and on RasMol 2.7.2, on RasMol 18.104.22.168, on RasTop 1.3, on RasMol version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb. Please read the file NOTICE for important notices which apply to this package and for license terms (GPL or RASLIC).
This version of RasMol is not in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol.
[18/03/2008] HJB graphics.h mswin31.c rasmol.c rastxt.c raswin.c x11win.c Add global InitWidth, InitHeight, InitXPos, InitYPos to support common implementation of command line options -height nnnn -width nnnn -xpos nnnn -ypos nnnn to control initial window size and position [18/03/2008] HJB x11win.c Redo Japanese and Chinese fontset logic as per suggestion by Mamoru Yamanishi [18/03/2008] HJB Imakefile Allow use of old X locale. [18/03/2008] HJB langsel_unix.c Switch Japanese for unix from SJIS to EUC-JP, introducing langsel_unix.c [21/02/2008] TPI actionmenu.gtk egg-macros.h eggfileformatchooser.c eggfileformatchosser.h graphics.h gtkwin.c Imakefile multiple.c printing-resolution.glade rasmol.c sizechooser.glade transfor.c wbrotate.c Addition of GTK interface by T. Ikonen, including new routines actionmenu.gtk egg-macros.h eggfileformatchooser.c eggfileformatchosser.h gtkwin.c printing-resolution.glade sizechooser.glade
[19/01/2008] HJB Release 22.214.171.124 created [18/01/2008] HJB command.c, maps.c, maps.h, molecule.c mswin31.c outfile.c outfile.h pixutils.c pixutils.h rasmac.c, repres.c Add LoadCCP4MapFile. Extend range of stereo angle to 60 degrees. Add GM notoggle command. Add code to avoid trying to reuse a zapped map. Increase default map resolution to 1 Angstrom. Change mapdata to void * and use memmove to allow multiple data types, add fields for number of grid divisions, map type, element size and element type. Add code to load and save maps in CBFlib format. Fix stereo. [16/01/2008] HJB vector.c wbrotate.c Fix multiple definitions of PI. [14/01/2008] LM infile.c Add include of string.h as per Ladislav Michnovic. [14/12/2008] HJB graphics.h Add buffers for slab and depth pixel-by-pixel cutoff values. [10/12/2007] GM langsel.c langsel.h languages/README.txt languages/genlanselall languages/langsel*.utf.c, tokens.c tokens.c Corrected japanese langsel encoding. It is now Shift_JIS.Added messages for NoToggle and ColourMode commands. Updated langsel README.txt. Add NoToggle and ColourMode commands [06/12/2008] GM command.h Add NoToggle and ColourMode variables. [25/11/2007] HJB cif_fract.c Rewrite calculation of matrix inverse.
[19/11/2007] HJB Release 2.7.4 created [19/11/2007] HJB abstree.c abstree.h Break out element identification from GetElemNumber into GetElemDescrNumber. Fix torsion angle calculation as per bug report and patch by Swati Jain. [19/11/2007] HJB applemac.c Add code to make languages sticky. Add register and donate menu items, make languages sticky and launch browsers. [19/11/2007] HJB cif_fract.c Correct calculation of matrix transforming orthogonal to fractional coordinates and rewrite matrix transforming fractional to orthogonal. [19/11/2007] HJB command.c command.h Add code for map commands. Make CommandError accessible from other routines. Add Raster3D write/save option. Allow proberadius of 6 Angstroms. Add Bulgarian, Chinese, Japanese and Russian commands. Allow spacefill up to 12 Angstroms. Allow mirror and rotate suboptions on write/save. [19/11/2007] HJB font.h, graphics.h Allow access to font parameters and support info [19/11/2007] HJB Imakefile Add use of CBFlib [19/11/2007] HJB infile.c Make sensitive to PDB version to allow for handling of remediated files, based on changes suggested by Huanwang Yang of the RCSB PDB in April 2007. [19/11/2007] GT langsel.c languages/ langsel.c restructured to be generated from separate language files in the directory languages/ [19/11/2007] HJB molecule.c molecule.h Add atom type processing and DA, DC, DG, DT, DI for remediated PDB DNAs, based on changes suggested by Huanwang Yang of the RCSB PDB in April 2007. [19/11/2007] HJB multiple.c multiple.h Manage map data for multiple molecules. Increase the number of molecules from 5 to 15. Increase the number of characters in the name to 33 characters. [03/12/2006] HJB outfile.c Clean up compilation warnings in outfile.c [19/11/2007] HJB outfile.c outfile.h Add Raster3D support based on code by V. Stanev. Partial Vector PS map support. [19/11/2007] HJB pixutils.h Fix stereo of ribbons and map surfaces. Protect against duplicate definition of Knot struct. Make ClipPolygon accessible. [19/11/2007] HJB rasmac.c rasmac.h Increase terminal window to 132 characters. Add About dialog. Clean up maps on exit. Add support for Russian, Bulgarian, Chinese and Japonese. Add register and donate browser calls. Add G4 CPU type. Extend export file types. [19/11/2007] HJB RasMac.r Update icons to new style. Extend Export menu to BMP..., GIF..., IRIS RGB..., PPM..., Sun Raster, PostScript, PICT..., Vector PS ..., Molscript ..., Kinemage ..., POVRay 3 ..., VRML ..., Ramachandran ..., Raster3D ..., RasMol Script .... Extend Apple menu to About RasMol..., RasMol Help ..., Register ..., Donate .... [19/11/2007] HJB rasmol.c Update to release 2.7.4 with map support. [19/11/2007] HJB script.c script.h Add code to write out scripts for maps. [19/11/2007] HJB string_case.c string_case.h Fix case sensistive of last character comparison of strcasecmp and strncasecmp. Add str255casecmp, strcasestr. [19/11/2007] HJB tokens.c tokens.h Add tokens for Average (MeanTok), Bulgarian (BulgarianTok), Chinese (ChineseTok), Contour (ContourTok = LevelTok), Generate (GenerateTok), Japanese (JapaneseTok), Level (LevelTok = ContourTok), Map (MapTok), Mask (MaskTok), Mesh (WireframeTok), Mirror (MirrorTok), New (NewTok), Next (NextTok), R3D or Raster3D (Raster3DTok), Resolution (ResolutionTok), Spacing (SpacingTok), Spread (SpreadTok), Width (SpreadTok), [19/11/2007] HJB transfor.c transfor.h Add map point colouring routines, ColourPointAttrib and ColourPointPotential. [19/11/2007] HJB x11win.c Extend Export menu to BMP ..., GIF ..., IRIS RGB ..., PPM ..., Sun Raster, PostScript, PICT ..., Vector PS ..., Molscript ..., Kinemage ..., POVRay 3 ..., VRML ..., Ramachandran ..., Raster3D ..., RasMol Script .... Enable and extend Help menu to About RasMol..., User Manual..., Register..., Donate.... Set locale for each langauge and use fontsets. Use table of languages versus fonts in langsel. Add About splash screen and revise popup logic to handle it. Change text metrics to allow for Chineses and Japanese. Try to make lack of access to shared memory non-fatal. [03/10/2007] PK molecule.c "RasMol - " string added to the title of the window. [03/10/2007] PK multiple.c Window title is updated when different molecule is selected. [02/02/2007] HJB rasmol.c Remove // comments for AIX build. Fix signed length conflict [01/03/2007] GT rasmol.c Chinese version. [23/12/2006] HJB x11win.c Detect remote X server that does not share memory [29/12/2006] HJB rasmol.c x11win.c Update x11win.c and rasmol.c to add links to list of browsers and to kill About dialog when the menu bar is selected [29/12/2006] HJB rasmol_install.sh Update rasmol_install.sh to allow recompilation of fonts on install to handle openwin and other old systems that can't handle byte-swapped bdf files, and add enviroment variable RASMOL_NOSPAWN to suppress spawn in intermediate xterm from rasmol_run.sh. -- HJB [23/12/2006] HJB rasmol_install.sh, rasmol_run.sh scripts Add new rasmol_install.sh and rasmol_run.sh scripts [29/11/2006] HJB raswin.idm Fix missing raswin.idm in src. [29/11/2006] HJB rasmol.c Add missing include of sys/stat.h in rasmol.c [10/12/2006] HJB x11win.c Additional updates for linux build with Russian, cleaning up X11 font selection for CP1251 and recovering when fonts are missing. -- HJB [03/12/2006] HJB x11win.c Mods for about screen under Linux -- HJB [28/11/2006] HJB x11win.c Changes for Russian and About dialog in unix [20/10/2006] HJB wbrotate.c Localize " not found!" message in RemoveBond and CreateBondAxis [16/09/2006] HJB x11win.c rasmol.c Start of RasMol Russian Translation Project based on translations by Gregory A. Pozhvanov of Saint Petersburg State University. [11/02/2006] HJB script.c script.h Add mirror and rotate options for VRML.
[21/04/2006] HJB rasmol.h RasMac.r raswin.rc Update version to 126.96.36.199 [21/04/2006] CC abstree.c render.c repres.c repres.h Fix by Clarice Chigbo to improve accuracy of distance calculations by changing from Long to double. Report model number. Use Long instead of short for monitors. [15/12/2005] HJB x11win.c Fix mouse runaway by removing conflict of HeldStep and HeldButton variable name use. [16/07/2005] HJB abstree.c infile.c render.c Correct sign errors in use of ztrl
[06/02/2005] HJB Release 2.7.3 created [21/01/2005] HJB molecule.c Correct XYZ input by capping atom types. Thanks to Stuart Prescott. [16/01/2005] HJB applemac.c, cmndline.c, command.c, command.h, infile.c, langsel.c, langsel.h, langsel_mac.c, molecule.c, molecule.h, mswin31.c, multiple.c, pixutils.c, pixutils.h, rasmac.c, rasmol.c, rastxt.c, raswin.c, render.c, render.h, repres.c, repres.h, tokens.c, tokens.h, transfor.h, x11win.c Base level of changes for Lee-Richards molecular surfaces. [12/01/2005] Clarice Chigbo repres.c, render.c, repres.h Correction to negative torsion angle monitors and to imprecise distance and angle monitors; limits the available range for distance monitors to approximately 327 Angstroms. [17/01/2005] Clarice Chigbo script.c Output CPKNEW in scripts [04/01/2005] Ricky Chachra command.c Fix to wireframe 0, ribbon 0, cartoon 0, backbone 0, strands 0 and trace 0 commands to work the same as these command with off instead of 0 [30/10/2004] Mamoru Yamanishi Imakefile, rasmol.c Used xforms to provide GUI for file open under X-windows [21/10/2004] Clarice Chigbo tokens.c, tokens.h Define CPKNEW token [20/10/2004] Clarice Chigbo transfor.c, transfor.h New CPK color table [26/04/2004] HJB cif.c correction to handling of blank immediately following initial quote mark. [26/04/2004] HJB vector.c correction to SubtractAtoms for bond rotation.
[07/05/04] HJB mswin31.c restored lost fix for intialization of ZRange and DialValue[8..9] and rebuilt raswin.exe. Thanks to Julien Hering. [14/02/04] HJB pixutils.c remove static from declaration of ClipVector. [14/02/14] HJB cif_stx.c remove trailing characters from #endif. [03/02/04] HJB Makefile.in Change transfer to transfor in 2 dependencies. Thanks to R. Harlow.
[26/01/04] HJB abstree.c Fix warning on sprintf calls with unused args, match long variables with %ld format descriptors. [26/01/04] HJB cif.c Add brackets to avoid compiler warnings on dangling elses. Fix cif_lex to parse 'O''' correctly. Change from WORD to CIFWORD to avoid conflict with windows.h. [26/01/04] HJB cif.h Change from WORD to CIFWORD to avoid conflict with windows.h. Add prototype for cif_free_handle. [26/01/04] HJB cif.stx.tab.c Change from WORD to CIFWORD to avoid conflict with windows.h. [26/01/04] HJB cif_ctonum.c Remove unused variable dndec [26/01/04] HJB cif_fract.c Remove unused variable kk [26/01/04] HJB cif_stx.c Change from WORD to CIFWORD to avoid conflict with windows.h. Add include of rasmol.h. [26/01/04] HJB command.c Initialize variables to avoid compiler warnings. Use %ld format for long variables. Fix RotMode == RotBond which should have been an assignment. Add parens on logical expressions. [26/01/04] HJB command.h Add prototypes for ResumePauseCommand, InterruptPauseCommand. [26/01/04] HJB graphics.h Add include of windows.h [26/01/04] HJB infile.c Removed unused ReadValue2. Add brackets to avoid compiler warnings on dangling elses. Initialize variables to avoid compiler warnings. [26/01/04] HJB langsel.c langsel_mac.c Add include of string.h [26/01/04] HJB molecule.c Add include of graphics.h. Change to %ld format for longs. Remove unused variables. Add brackets to avoid compiler warnings on dangling elses. [26/01/04] HJB molecule.h Add prototype of TestDisulphideBridge. [26/01/04] HJB multiple.c Fix reversed comment terminator. Add include of string.h. Add brackets to initializer to match structure. [26/01/04] HJB multiple.h Add prototype of ReRadius. [26/01/04] HJB outfile.c Initialize variables to avoid compiler warnings. Change to %ld for long. [26/01/04] HJB pixutils.c Initialize variables to avoid compiler warnings. Removed unused variables. [26/01/04] HJB pixutils.h Add prototypes of DrawTwinLine, ClipLine, ClipTwinLine, ClipDashLine, DrawTwinVector, ClipVector, ClipTwinVector, ClipDashVector. [26/01/04] HJB rasmol.c Add parens to avoid compiler warning. [26/01/04] HJB rasmol.h Set version and date. Add include of stdlib.h for malloc. [26/01/04] HJB render.c Change the handling of very long longs to avoid a compiler warning. Use %ld format for longs. [26/01/04] HJB repres.c Remove unused variables. Use %ld format for longs. Initialize variables to avoid compiler warnings. [26/01/04] HJB repres.h Add prototype of LoadDotsFile. [26/01/04] HJB script.c Add include of string.h. Use %ld format for longs. Initialize variables to avoid compiler warnings. Remove unused variables. Fix sign of trailing bits on VRML z coordinates. [26/01/04] HJB script.h Add prototype of WritePOVRay3File. [26/01/04] HJB tokens.h Add parens in definition of IsImageToken. [26/01/04] HJB transfor.c Add parens for logical expression. Remove unused variables. Initialize variables to avoid compiler warnings. [26/01/04] HJB transfor.h Add prototype of DefineShade, RMat2RV, RV2RMat. [26/01/04] HJB wbrotate.c Add include of cmndline.h. Remove unused variables. Initialize variables to avoid compiler warnings. Use %ld format for longs. Add value for a returns that need them. [26/01/04] HJB x11win.c Initialize variables to avoid compiler warnings. Add brackets to avoid compiler warnings on dangling elses. [14/04/02] HJB Imakefile Update to allow scripts to make multiple pixel depths by setting PIXELDEPTH to 8, 16 or 32 externally. Add default flags for various HP architectures. [13/04/02] HJB cif.c Reduce warnings by casting uses of size_t. [13/04/02] HJB cif_ctonum.c Reduce warnings by casting to int for pointers indptr-test. [13/04/02] HJB command.c Reduce warnings by explicit use of long (rather than Long) for fpos, and casting to size_t for comparisons, etc. [13/04/02] HJB infile.c In ProcessPDBBond, match types of srcatm and dstatom by changing from int to Long, casting to size_t for comparisons, etc. [13/04/02] HJB molecule.c Change MemSize from int to size_t. [13/04/02] HJB rasmol.c Change AdviseLen from int to size_t, change socket to xsocket, change __hpux to HPUX_LEGACY [13/04/02] HJB rasmol.h Add HPUX_LEGACY for old style hpux select. [13/04/02] HJB render.c Make test of sizeof(Long) > 4 conditional on not defining _LONGLONG. Make some changes from Long to long, etc. [13/04/02] HJB x11win.c Cast some pointer diffs to int, change some Long to long, etc. [29/06/01] HJB command.c Correct logic for inline load of a new molecule from data file treated as a script. [21/04/01] HJB all Fix credit for initial Spanish translation. Thanks to E. Martz. [19/04/01] HJB command.c Post release fix to handling of load inline in windows version due to problem with STRICT logic. Thanks to Jan Reichert
for pointing out the problem. [18/04/01] HJB command.c Post release fix to handling of load inline in UCB multiple molecule environment. Thanks to Jan Reichert for pointing out the problem.
[14/04/01] HJB script.c Correct error in writing scripts with partial use of spacefill. Thanks to Steven Vik
for reporting the problem. [14/04/01] HJB rasmol.doc, itasmol2721.hlp, esrasmol.html Updated manuals for 188.8.131.52. [02/04/01] HJB abstree.c, abstree.h Increase space for atom names from 4 to 12 characters. [02/04/01] HJB applemac.c Add symbolic ZRange, add 2 dials. See [12/01/01] changes for langsel. [02/04/01] HJB cmndline.c, cmndline.h Reworked all exits on mouse motion processing to leave values in DialValues or WRot..., etc depending on RotMode. Made HeldButton a global for future reference. [02/04/01] HJB command.c, rasmol.c, rasmac.c, raswin.c Change stereo command to cycle cross-wall-none. [02/04/01] HJB command.c, script.c, transfor.c Rework output of rotation information. [02/04/01] HJB infile.c Increase limit on atom names for CIF from 4 to 12 characters. [02/04/01] HJB langsel.c langsel_mac.c Add French (thanks to Jean-Pierre Demailly ) and Italian (Giuseppe Martini and Giovanni Paolella with contributions by: A. Davassi, M. Masullo, C. Liotto, G. Paolella, G. Martini. Adapt to 2.7.2 menu structure. [02/04/01] HJB mswin31.c Removed "Printing Completed" message. [02/04/01] HJB multiple.c Save DotPtr to fix misplaced dots in multiple molecules. Save LastTX, LastTY, LastTZ, LocalRadius, ShiftS, XlateCen. Make "Insufficient memory" message be language dependent MsgStrs[StrMalloc] [02/04/01] HJB outfile.c, pixutils.c, repres.c Rework backclipping separating ZOffset from new DepthValue, define BitBack [02/04/01] HJB tokens.c Added the following tokens relative to 2.7.2, includes tokens added for 184.108.40.206: ASSE AxesTok ASSI AxesTok CADENA ChainTok CADENAS ChainTok CATENA ChainTok CATENE ChainTok COPY CopyTok DEPTH DepthTok DIBUJO CartoonTok DIBUJOS CartoonTok E AndTok EJE AxesTok EJES AxesTok ELANCE BondTok ELANCES BondTok ELICHE HelixTok ENGLISH EnglishTok ELICHE HelixTok ESQUELETO BackboneTok ETIQUETA LabelTok ETIQUETAS LabelTok ETICHETTA LabelTok ETICHETTE LabelTok FILODIFERRO WireframeTok FILDIFERRO WireframeTok FILI StrandsTok FRENCH FrenchTok GIRO TurnTok GIROS TurnTok GRUPO GroupTok GRUPPO GroupTok HEBRAS StrandsTok IMAGE ImageTok ITALIAN ItalianTok MOSTRAR DisplayTok NASTRO RibbonTok NASTRI RibbonTok PASTE PasteTok POSITION PositionTok RIEMPIMENTO SpacefillTok SALIR ExitTok SCHELETRO BackboneTok SELECTION SelectionTok SHADEPOWER ShadePowerTok SPANISH SpanishTok TODO AllTok TUTTO AllTok VIEW ViewTok VIGNETTA CartoonTok VISUALIZZA DisplayTok [02/04/01] HJB transfor.c Rework interaction of mouse, local rotation and world rotation to make horizontal mouse motion of individual molecule rotate horizontally even when outer world rotation creates a tilt. Restores incremental mouse motion effects similar to what was in effect for 2.7.1, but with world rotations. Reworked RasTop centering to restore 2.7.2 behavior -- defaults to center the new rotation on the screen. [02/04/01] HJB several Make dial indices symbolic. [02/04/01] HJB wbrotate.c, wbrotate.h Rework interaction of mouse and world rotation to make horizontal mouse motion of individual molecule rotate horizontally even when outer world rotation creates a tilt.
Note: These mods do not reflect the complete source of RasTop 1.3.
[31/01/00] 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" [30/01/00] PV command.c
Added command "select view" and corresponding code, which allows to select a part of a molecule based on screen display. [16/01/00] PV cmndline.c In PerformMouseFunc() corrected MM_CLIP to access clipping with the mouse, added MM_DEPT to access backclipping (depth) with the mouse. [16/01/00] PV transfor.h, transfor.c, token.h, token.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. [03/01/00] PV transfor.c Fixed bug (and modified) function Power() to handle Specpower [12/14/99] PV Added variables ShiftS and UseAutoDepthCue that adjust DepthCue with slabbing. [14/12/99] PV transform.c 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. [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()) [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. [21/09/99] PV command.c, render.h, render.c, transfor.h, transfor.c Added four new picking modes: select an atom: PickAtom; 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. [Note by HJB 02/04/01 -- The UCB and 2.7.2 bond picking was used in 220.127.116.11 instead of the RasTop version] [22/09/99] PV abstree.h, abstree.c First step for saving atomsets & identifiers in RasMol scripts (SetSize to 100 and SymEntry and SymbolTable in header). [21/09/99] PV cif.h Fixed missing declaration of cif_parse in cif.h [21/09/99] PV cmndline.c In ProcessCharacter()) added ESC (0x1b) character to interrupt script pausing. [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 infile.c Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0) - explicited all conversions long to short in infile.c /*casting*/ [21/09/99] PV pixutils.c Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0) - fixed casting in drawstar() and clipstar() in 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. [14/07/99] PV abstree.c transfor.c (Adapted from RasTop 1.3) Added shortcuts for direct evaluations of atomsets (BuildAtomSet(), SelectZoneExpr()). [14/07/99] 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. [10/07/99] PV cif.c Fixed memory allocation bug in cif_make_handle
[28/08/00] HJB all Updates to comments, resources, etc for preliminary testing release. [21/08/00] HJB abstree.c, abstree.h Change type Atom to RAtom to avoid conflicts with X. Offset all uses of xorg, yorg, zorg databse entried with fxorg, fyorg, fzorg database entries for UCB bond rotation. Change char* strings to unsigned char* strings to allow for extra UCB Angstrom and degree symbols. [21/08/00] HJB applemac.c Change from use of toolbar settings to use of RotMode. Add new "Settings" menu. [21/08/00] HJB cmndline.c Adapt GSG code from UCB mods for mouse moves, to make the moves control bond rotation, molecule rotation, or world rotation, but change from use of toolbar settings to use of RotMode [21/08/00] HJB command.c Add new error message (ErrNoBond) for "Bond for rotation not picked". Add new parameter for alternate conformer bond waist radius. Adapt to fxorg, etc. offsets. Adapt GSG UCB pick bond tool bar button to a command line command. Add show centre, show rotation, show translation and show zoom commands. Add bond, unbond commands. Add rotate bond, rotate molecule, rotate all command. [21/08/00] HJB command.h Add space after "__huge" [21/08/00] HJB font.h Adapt GSG UCB mods characters for Angstrom and degree to be additional symbols, not repalcements. [21/08/00] HJB graphics.h Add new redraw flag, "RFRotBond" to signal that a bond rotation is involved, and add it to RFRotate, RFApply and RFInitial. Add ZRange. Move main X window definitions into this header to facilitate toolbar development. [21/08/00] HJB infile.c, infile.h Change all Atom types to RAtom. Add xorg, etc. offsets on all coordinate calauclations. Move GroupPool definition to header. [21/08/00] HJB molecule.h and all referring files Change type Atom to RAtom to avoid conflicts with X. Add fxorg, fyorg, fzorg database entries for UCB bond rotation offsets. [21/08/00] HJB multiple.c Remove all use of the toolbar, converting to menu. Detect last element of file name string. Update VarList for current variables. Change to ANSI C prototypes. Move revised DrawMoleculeList from GSG's UCB toolbar.c into multiple.c, but drop list only into MolName. [21/08/00] HJB wbrotate.c, wbrotate.h Remove all use of the toolbar, converting to menu. Change to ANSI C prototypes. Revise bond and world rotation logic to use full rotation, nor increment, for improved accuracy. Change Bond rotation logic to preserve nesting of bonds without changing the original coordinates. Add database of selected bonds and logic to add bonds on the fly and remove them. [21/08/00] HJB vector.c, vector.h Change to ANSI C prototypes. Replace Vector and Matrix with their array definitions for clarity. [27/02/00] HJB transfor.c, transfor.h Add alternate conformer bond radius to EnableWireFrame [23/02/00] HJB infile.c Fix *- for - typo in XYZ and MOL2 input of coordinates [23/02/00] HJB molecule.c Fix D2O to DOD mapping. Thanks to Brian W. Beck. [23/02/00] HJB pixutils.c New code for alternate conformer bonds. [23/02/00] HJN raswin.c Update WinMail entry to WINAPI [29/01/00] HJB molecule.c Comment out chain by chain reset of bonding to allow for het groups after TER at expense of slower bonding. [29/01/00] HJB mswin31.c Update printer logic for modern windows specs. [29/01/00] HJB rasmac.c Fix reference of monaco font. [15/07/99] HJB (for AR) raswin.c Add check for \r. Thanks for Andrew Raine. [15/07/99] RS raswin.c Add .ML2 and .SY2 extensions for Sybyl and MOL2.
Note: These mods do not reflect the complete source of UCB RasMol. In particular toolbar.h and toolbar.c have not been used in this pass, and the full source of UCB RasMol has not yet been recovered.
[30/11/95] GSG rasmac.c Hide command window. Add help screen menu logic. Add hooks to load multiple molecules. Add toolbar menu to Windows menu. Make mouse moves control bond rotation, molecule rotation or world rotation depending on tool bar button choices. Same for scroll bars. [29/11/95] GSG applemac.c Change default background for printing to white. Hook scroll bar H values to bond angle (BRotValue), molecule rotation angle (DialValue) or world rotation angle (WRotValue) depending on toolbar settings. Hook scroll bar V values to molecule rotation angle (DialValue) or world rotation angle (WRotValue) depending on tool bar settings. Allow file open when less than MAX_MOLECULES molecules. [21/08/00] GSG font.h Add characters for Angstrom and degree as replacements for vertical bar and tilde. [16/11/95] GSG render.c, render.h Add PickBond. Add hooks to draw multiple molecules. Automatically switch to the molecule of any picked atom. Add monitor for picked distance, angle or torsion angle. [14/11/95] GSG transfor.c Add hooks for bond rotation and global rotation. [14/11/95] GSG vector.c, vector.h, wbrotate.c, wbrotate.h New routines introduced with UCB mods to allow for bond rotations and global rotation. [14/11/95] GSG infile.c Add fxorg, fyorg, fxorg for MDL molecule input only. [14/11/95] GSG molecule.c, molecule.h Add fxorg, fyorg, fxorg and list of bonds to atom database for world and bond rotation. [11/11/95] GSG multiple.c, multiple.h New routine introduced with UCB mods to allow for multiple molecules. [10/11/95] GSG tokens.c,tokens.h Add MoleculeTok. [10/11/95] GSG repres.h Add flag for units to Monitors. [09/11/95] GSG command.c, command.h Add hooks for multiple molecules. Log background status to allow default white print background. Add molecule command. [09/11/95] GSG rasmol.c Add initialisation for multiple molecules.
[21/01/01] FGR, HJB langsel.c, langsel_mac.c, mswin.c, applemac.c Installed translations for Edit menu on mac and PC provided by Fernando Gabriel Ranea. [17/01/01] FGR, HJB langsel.c, langsel_mac.c Corrections to translations by Fernando Gabriel Ranea, installed by HJB with revisions to menu bar accelerators. [12/01/01] HJB applemac.c Added include of langsel.h. Added routine ReWriteStr255 to rewrite menu bar items in place and tostr255 to convert other menu items strings to Pascal form for use in SetmenuItemText. Set up ReDrawWindow to refresh all menu strings and then redraw the menu bar. Note that the rewrite of the main menu bar is _very_ risky and may not survive system changes. [12/01/01] HJB command.c Added include of langsel.h. Remove redundant ErrorMsg array and Err... definitions. Change messages to reference MsgStrs. Add English and Spanish as commands calling SwitchLang. [12/01/01] HJB infile.c Fix coordinate typo in load of XYZ and Mol2 molecules. [12/01/01] HJB langsel.c, langsel_mac.c, langsel.h New routines to carry multi-lingual translations. Many thanks to Fernando Gabriel Ranea for the bulk of the Spanish translations, and for creating the initial Spanish version of RasMol 2.7.1. Note that langsel.c uses the ANSI character set, while lansel_mac.c uses the Macintosh character set. [12/01/01] HJB molecule.c Added include of langsel.h. Changed messages to reference MsgStrs. Refixed D2O misparse, which had been previously fixed. Mod had been lost. [12/01/01] HJB mswin31.c Added include of raswin.idm and langsel.h. Included partial update to printer logic. Added ReDrawWindow as rewrite of menus with ModifyMenu and RemoveMenu/AppendMenu calls. [12/01/01] HJB rasmac.c Added include of langsel.h. Added SwitchLang(English) calls for initialization to main routine. [12/01/01] HJB rasmol.c Add fix for broken math routines by referencing atan2. [12/01/01] HJB rasmol.h Added include of langsel.h. Added SwitchLang(English) calls for initialization to main routine. [12/01/01] HJB raswin.c Added include of langsel.h. Changed font of command window to ANSI character set. Changed most messages to reference MsgStrs. Add SwitchLang(English) calls for initialization to WinMain. [12/01/01] HJB x11win.c Restructured MenuItem and BarItem to make .text, .pos and .len indirect, so that they can be fetched from MsgStrs, MsgAuxl and MsgLens. The .pos field is used to specify the character offset of the acceleration key. The main menu bar may now have non-zero offsets. All the menu items have been changed to MsgStrs[StrM...] referecences, and added include of langsel.h. Added ReDrawWindow simply as a call to ReSizeWindow. This is overkill, but appropriate for these infrequent calls. [12/01/01] HJB tokens.h Added tokens EnglishTok and SpanishTok. [12/01/01] HJB graphics.h Added prototype of ReDrawWindow, a system-dependent call to be used after updating menus on language changes. [12/01/01] HJB cmndline.c Added include of langsel.h, changed prompts as follows: "PDB file name:" MsgStrs[StrPrmtPDB] "Image file name:" MsgStrs[StrPrmtImg] "Molecule file name:" MsgStrs[StrPrmtMol] [12/01/01] HJB tokens.c Added the following tokens: CADENA ChainTok CADENAS ChainTok DIBUJO CartoonTok DIBUJOS CartoonTok E AndTok EJE AxesTok EJES AxesTok ELANCE BondTok ELANCES BondTok ENGLISH EnglishTok ESQUELETO BackboneTok ETIQUETA LabelTok ETIQUETAS LabelTok GIRO TurnTok GIROS TurnTok GRUPO GroupTok HEBRAS StrandsTok MOSTRAR DisplayTok SALIR ExitTok SPANISH SpanishTok TODO AllTok [26/12/99] HJB mswin31.c Do not reset Voxel Data for each chain. [02/10/99] HJB molecule.c Update printer logic.
[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
[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.
[22/04/99] HJB Announce RasMol 18.104.22.168 on email@example.com, firstname.lastname@example.org, email@example.com [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.
[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
[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
[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).
[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.
[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
The complete version 2 change history is in the directory ChangeLog