Rasmol Mac Os X Download

For Mac OS X incl. Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. Mage and Kinemages. Interactive molecular display for research and educational uses. There is no way before OS X of issuing the equivalent of the 'rasmol -script' command. Instead the Mac version of rasmol depend on the 'type' information for the file rasmol scripts are type RSML (creator RSML), pdb files are TEXT (creator RSML). Welcome to the RasMol and OpenRasMol web site. This site was established in mid-September 2000 to provide a home for developers of Open Source versions of RasMol. In May 2002, it also became a home page for users of RasMol. RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992. It runs in Windows, Mac OS, Linux, and Unix. Using PyMOL is surprisingly easy, even if you lack knowledge of chemistry. The interface is well laid out and fairly intuitive, considering the program.

Based on RasMol 2.6byRoger Sayle
Biomolecular Structures Group,Glaxo Wellcome Research & Development,Stevenage, Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright © Roger Sayle 1992-1999
and Based on Mods by
AuthorVersion, DateCopyright
Arne MuellerRasMol 2.6x1 May 1998© Arne Mueller 1998
Gary Grossman and
Marco Molinaro
RasMol 2.5-ucb November 1995
RasMol 2.6-ucb November 1996
© UC Regents/ModularCHEM
Consortium 1995, 1996
Philippe ValadonRasTop 1.3 August 2000© Philippe Valadon 2000
Herbert J. BernsteinRasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999
RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
© Herbert J. Bernstein 1998-2005

with RasMol 2.7.3 incorporating changes by Clarice Chigbo, Ricky Chachra,and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part bygrants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. NationalScience Foundation and grant DE-FG02-03ER63601 from the U.S. Departmentof Energy.

and Incorporating Translations by
AuthorItemLanguage
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 ManualSpanish
José Miguel Fernández Fernández2.7.1 ManualSpanish
Fernando Gabriel Ranea2.7.1 menus and messagesSpanish
Jean-Pierre Demailly2.7.1 menus and messagesFrench
Giuseppe Martini, Giovanni Paolella,
A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
Rasmol app
This Release by
Herbert J. Bernstein,Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright © Herbert J. Bernstein 1998-2005

The original RasMol manual was created by Roger Sayle. In July 1996,Dr. Margaret Wong of the Chemistry Department, Swinburne Universityof Technology, Australia, made extensive revisions to the RasMol 2.5manual to accurately reflect the operation of RasMol 2.6. Eric Martzof the University of Massachusetts made further revisions. In May1997, William McClure of Carnegie Mellon University reorganized theHTML version of the manual into multiple sections which could bedownloaded quickly and added use of frames. Portions of the 2.7.1version of the RasMol manual were derived with permission fromWilliam McClure's version using Roger Sayle's rasmol.doc forversion 2.6.4 as the primary source. Changes were made inAugust 2000 for RasMol version 2.7.2, January 2001 for RasMolversion 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 andFebruary 2005 for RasMol version 2.7.3.

Documentation Last Updated 19 April 2005
Edited by Herbert J. Bernstein and Frances C. Bernstein

Translations

Thanks to the efforts of José Miguel FernándezFernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada.España (jmfernan@ugr.es)) a translation of theManual for Rasmol version 2.7.1 into Spanish is now available.La traducción española del manual de laversión de la Dra. Wong revisada por Eric Martz fue realizada porIsabel Serván Martínez y José Miguel FernándezFernández. La actual traducción del Manual de RasMol 2.7.1ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández.

Thanks to translations by Fernando Gabriel Ranea in late 2000and early 2001, RasMol is nowcapable of rendering most menu items and messages in Spanish. Jean-Pierre Demailly provided Frenchtranslations of menus and messages in January 2001. Giuseppe Martini and Giovanni Paolella with contributions by A. Davassi, M. Masullo and C. Liotto provided Italiantranslations of menus and messages in March 2001.

THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******

IMPORTANT - Copying and Distribution

This version is based in directly on RasMol version 2.7.2.1.1,on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMolversion 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version2.6.4, and RasMol 2.5-ucb and 2.6-ucb.

Please read the file NOTICE forimportant notices which apply to this package and forlicense terms (GPL or RASLIC).

Rasmol Program

Contents

Rasmol Mac Os X download free. full

  • Directories
    • ChangeLog -- Full ChangeLog directory
    • src -- source code
      • mac -- Macintosh build directory
      • mswin -- Windows build directory
    • doc -- documentation
    • data -- sample data files

Introduction

This posting is made to announce the releases of RasMol version2.7.3. This release is based on RasMol 2.7.2.1.1,the final reference release for the 2.7.2 series. The changes for the2.7.3 release include:

  • Adjustment to the mouse handling for a better, more natural feel. Our thanks to C. Chigbo for the suggestion.
  • Correction to cif.c for blanks after an initial quote mark.cif.c.patch
  • Correction to mswin31.c to restore lost initializations of ZRangeand DialValue[8..9].mswin31.c.patch
  • Correction to vector.c for nested bond rotations.vector.c.patch
  • Modifications by Mamoru Yamanishi to Imakefile and rasmol.c to use xformsfor GUI file open. xforms.patch.This patch needs the opens source xforms 1.0.90 library bySteve Lamont (see the source at http://savannah.nongnu.org/download/xforms/xforms-1.0.90.tar.gz).The cummulative patch is given in the link above. The individual patchesare available at xforms/
  • Correction to molecule.c to correct input of xyz files. Thanksto Stuart Prescott. molecule.c2.patch.(Revised 20 Jan 2005).
  • Revision to CPK colors by C. Chigbo.cpknew.patch.The new colors are called CPKNEW. The current CPK colors remain availableas CPK. (Revised 16 Jan 2005 by HJB).
  • Correction to negative torsion angle monitors and toimprecise distance and angle monitors by C. Chigbo. datconsis.patch.(Revised 16 Jan 2005).This patch corrects the display of negative torsion angles caused by use ofthe unsigned short type, and correctys imprecise distance and angle displays.This extends the original patch which was just for torsion angles (torsion.patch).A side effect of this change is to limit the available range for distance monitors to approximately 327 Ångstroms.
  • Initial code for display of solid Lee-Richards molecular surfaces. surface3.patch.(Rev 20 Jan 05).This patch adds the basic code for display of Lee-Richards surfaces with anew Molecular Surface menu item, and surface molecule <probe radius> andsurface solvent <probe radius> commands. Two other, related, major patchesare pending that depend upon this one: code by P. Zhivkov to simulatesurfaces efficiently by blurring and code to display surfaces using OpenGL.
  • Corrections of ribbons 0, etc. commands by R. Chachra. comb3.patch.(Revised 18 Jan 05).With this patch, the wireframe 0, ribbon 0, cartoon 0,backbone 0, strands 0 and trace 0 commands work the same as thesecommand with off instead of 0.
Rasmol software download

The 2.7.2.1.1 release was the final reference release for the2.7.2 series prior to the creation of version 2.7.3. For mostusers there should be no operational changes from version2.7.2.1, except for the correction to the loading of PDBexchange dictionary CIFS.

Post release patches to command.c were included to fix thehandling of load inline in the UCB multiple molecule environment. In addition conditional code controlled by STRICT was disabled to restoreoperation of load inline under windows. Thanks to Jan Reichert <jr@imb-jena.de> for pointing out these problems. Thanks to E. Martz<emartz@microbio.umass.edu> for pointing out an error in the Spanishtranslation credits which has been corrected. Thanks to a report by Julien Hering, the omission of a prior fix to the MS Windowsversion was found and corrected on 7 May 2004.

The April 2001 posting was made to announce the release of RasMol version 2.7.2.1, whichmade the following changes to RasMol 2.7.2, incorporating changes fromRasMol 2.7.1.1 and some changes from RasTop 1.3:

  • Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol 2.7.2.1.
  • Rewrite of the mouse handling and rotation logic to correct theproblems in 2.7.2 and make the feel of 2.7.2.1closer to that of RasMol 2.7.1.
  • Addition of French menus and messages
  • Addition of Italian menus and messages
  • Adoption of picking for selection of atoms, groups or chains fromRasTop 1.3.
  • Adoption of backclipping from RasTop 1.3
  • Adoption of shadepower command for glassy surfaces from RasTop 1.3
  • Change of the menu stereo option to rotate cross-wall-none
  • Allow longer atom names (12 characters) in CIFs.

The release of RasMol version 2.7.1.1 made the following changes to RasMol 2.7.1:

  • Introduction of a multilingual structure for RasMol.
  • Population of messages and menu lists for English and Spanish.
  • Upgrade of some of the Windows printer logic
  • Correction of coordinate handling for Mol2 and XYZ coordinates
  • Fix to the parsing of D2O.
That was an interim release to facillitate testing of the new multilingualcapabilities. Our thanks to Fernando Gabriel Ranea for doing the hard work of creating an initial Spanish translation of RasMol 2.7.1.We have created this new version to allow on-the-fly switching among langauges.Use the command 'Spanish' to request Spanish messages and menus, and 'English'to return to the original English format.Corrections and translations for additional languagesgreatly appreciated.

The release of RasMol version 2.7.2,made the following changes to RasMol 2.7.1:

  • Incorporation of some of the code from the UCB RasMol variants.Out thanks to Eileen Lewis and Marco Molinaro for their cooperationin contributing the UCB Enhanced RasMol code for incorporationinto the RasMol 2.7 series.
  • Code to represent bonds in and to alternate conformers witha narrowed portion in the middle of each bond.
  • An attempt to fix some of the chirality reversals in some of theoutput modes.
  • Fixes for some of the problems reported since the last release.

This release does not include the toolbar from the UCB mods. In orderto resolve some cross-platform issues we have started incorporation ofthe UCB code for multiple molecules and bond rotation by adding tothe command interface and to the menus. We expect to be able toadd a toolbar in a future release.

This release is not fully debugged and has some serious problems. Thisrelease is intended for testing and experimentation and not forproduction use. Comments and suggestions would be appreciated. Weare aware fo the following deficiencies:

  • RasMol may have difficulty in allocating colors for moleculesafter the first. The fix for this interacts with some otherpending changes, and should be ready for the next release.
  • As has been true for all recent versions, the stereo mode defaultsto cross-eyed, which is inconvenient for many users. The next releasewill allow cross-eyed and wall-eyed stereo to be selected from the menus.
  • Printing under windows is not working for many modern systems.We hope to have a fix for the next release.
  • The fixes for several of the bugs reported against RasMol 2.7.1 havenot been incorporated into RasMol 2.7.2 yet. Our apologies. If youpreviously reported a bug in RasMol 2.7.1 which still exists in 2.7.2,you may resubmit your report, but there is no need to do so.

The release of RasMol version 2.7.1made the following changes to RasMol 2.7.0:

  • The ability to automatically mark non bonded atoms in wireframe and stick displays. Our thanks to R. Curtis Haltiwangerfor suggesting this change.
  • The ability to use a proportionally spaced font and to draw labelswith heavier strokes. Our thanks to Eric Martz for suggesting this change.
  • The ability to auto-recognize PDB vs. CIF and mmCIF datasets.
  • Extensive updating to the manual. Our thanks to William McClure,Margaret Wong, Eric Martz and Frances Bernstein.
  • Updating the canvas title with the PDB ID code and EXPDTA information,so models will be clearly distinguished from experimental data.Our thanks to Helen Berman for suggesting this change.
  • The ability to report coordinates.
  • Additions to the list of pre-defined colours.
  • Improved accuracy of coordinates in pseudo-PDB output.
  • Fixes to the centering logic.

RasMol version 2.7.0.1 was atechnically minor, but operationally critical upgrade to version 2.7.0,correcting a serious error in the selection logic introduced in the processof merging versions to create version 2.7.0.

RasMol version 2.7.0 combined Roger Sayle's version 2.6.4 with Herbert Bernstein's CIF modified version 2.6_CIF(Rev 2) and with Arne Mueller's version 2.6x1. Thiscombined version allows selection by alternate conformers as well asby models, production of Ramachandran printer plots (as in F. Bernstein'sfisipl), and access to A. Mueller's POVray output as POVray3 in addition tothe existing POVray version 2 output. (POVray3 should not be usedin the PC or Mac version, yet).

RasMol version 2.6x1 was an upgrade to RasMol by Arne Mueller to add code to allow listing of information about the chains, groups oratoms in a selection, listing of phi-psi, allow selection by cis angle cutoff, and to provide a POV-Ray version 3 output.

RasMol version 2.6.4 was a major code cleanup and reorganization by RogerSayle, dropping obsolete non-ANSI C options and providing speed improvments.

RasMol version 2.6_CIF(Rev 2) added pre-compiled binaries forOpenVMS 7.1 (DEC Alpha) and OpenVMS 6.2 (DEC VAX) and replaced the binaryfor 68K Apple MacIntoshes in RasMol version 2.6_CIF(Rev 1).

Rasmol version 2.6_CIF(Rev 1) wasa minor update to RasMol version 2.6_CIF, which added support for alternateconformer coloring of small molecule CIFs, using _atom_site_disorder_group,recognizes requests for bonds which have neither atom names nor atom numbers,ensures zapping of existing bonds when connect command is used.

RasMol version 2.6_CIF added several new features to RasMol:

  • Support for reading IUCr CIF and mmCIF format;
  • Coloring for alternate conformers and multiple NMR models;
  • Display of all NMR models in a data set.

This version is available for the Apple Macintosh and PowerMac in addition to UNIX, VMS and Microsoft Windows versions. However, becauseof limitations in the memory management under MacOS, very largemultiple NMR model datasets are not supported on the Mac or PowerMac atthis time.

For a complete list of changes from RasMol 2.6 refer to the distribution's 'ChangeLog'.

For installation instructions see 'INSTALL'.

For a list of open issues in this version, see 'TODO'. Roger Sayle'sprior list of pending projects is in 'PROJECTS'.

RasMol is a molecular graphics program intended for the visualisationof proteins, nucleic acids and small molecules. The program is aimed atdisplay, teaching and generation of publication quality images. Theprogram has been developed at the University of Edinburgh'sBiocomputing Research Unit and the Biomolecular Structures Group atGlaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats andinteractively displays the molecule on the screen in a variety of colourschemes and representations. Currently supported input file formatsinclude Brookhaven Protein Databank (PDB), Tripos' Alchemy and SybylMol2 formats, Molecular Design Limited's (MDL) Mol file format,Minnesota Supercomputer Center's (MSC) XMol XYZ format, CHARMm format,MOPAC format, CIF format and mmCIF format files. If connectivityinformation and/or secondary structure information is not contained inthe file this is calculated automatically. The loaded molecule may beshown as wireframe, cylinder (drieding) stick bonds, alpha-carbontrace, spacefilling (CPK) spheres, macromolecular ribbons (eithersmooth shaded solid ribbons or parallel strands), hydrogen bonding anddot surface. Atoms may also be labelled with arbitrary text strings.Alternate conformers and multiple NMR models may be specially colouredand identified in atom labels. Different parts of the molecule may bedisplayed and coloured independently of the rest of the molecule orshown in different representations simultaneously. The space fillingspheres can even be shadowed. The displayed molecule may be rotated,translated, zoomed, z-clipped (slabbed) interactively using either themouse, the scroll bars, the command line or an attached dials box.RasMol can read a prepared list of commands from a `script' file (orvia interprocess communication) to allow a given image or viewpoint tobe restored quickly. RasMol can also create a script file containingthe commands required to regenerate the current image. Finally therendered image may be written out in a variety of formats includingboth raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfileor as a MolScript input script or Kinemage.

RasMol will run on a wide range of architectures and systems includingSGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBMRS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBMPC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD),Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DECWindows). UNIX and VMS versions require an 8bit, 24bit or 32bit XWindows frame buffer (X11R4 or later). The X Windows version of RasMolprovides optional support for a hardware dials box and acceleratedshared memory rendering (via the XInput and MIT-SHM extensions) ifavailable.

Reports of builds and/or problems on various platforms appreciated.

Source Code and Binaries

The complete source codeand user documentation of RasMol 2.7.3 may be obtained byanonymous FTP at:

or on the web at:

The source code and documentation arestored in several files appropriate for the receiving operating system.Please read the 'README' file in the distribution directory. See the tablebelow for appropriate binaries. Mac and Windows binaries are no longerincluded on the tar.Unix and VMS users should retrieve the same file for source code anddocumentation, and one or more of the following pre-compiled binaries:WARNING: ALL binaries are gzipped!!!. Uncompressedbinaries are also available in the second section of each page.

HP: RasMol.HP
Linux (Mandrake 9, i686): RasMol.LINUX
Mac: RasMol.MAC
MS Windows: RasMol.MSWIN
RS/6000: RasMol.RS6K
SGI: RasMol.SGI

You will need both an appropriate binary and a copy of rasmol.hlp for eachsystem, and, under Windows, a copy of raswin.hlp for the WinHelp sub-system.

Please remember to use'binary' mode when transferring these files between systems. Check thatthe file size is the same before and after transfer.

Any comments, suggestions or questions about thismodified version of RasMol should be directed torasmol@bernstein-plus-sons.com.

| OpenRasMol |Copying and Distribution |Contents |Installation Instructions |
| Changes |Things To Do |Introduction | Source Code and Binaries |Latest Windows Installer |External Packages |
| RasMol Manual |Spanish Translation of RasMol Manual | Italian Translation of RasMol 2.7.1 Help File |
| Make a Donation | Release README |
Updated 31 December 2006.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA

Rasmol Software Download


yaya@bernstein-plus-sons.com
Based on RasMol 2.6byRoger Sayle
Biomolecular Structures Group,Glaxo Wellcome Research & Development,Stevenage, Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright © Roger Sayle 1992-1999
and Based on Mods by
AuthorVersion, DateCopyright
Arne MuellerRasMol 2.6x1 May 1998© Arne Mueller 1998
Gary Grossman and
Marco Molinaro
RasMol 2.5-ucb November 1995
RasMol 2.6-ucb November 1996
© UC Regents/ModularCHEM
Consortium 1995, 1996
Philippe ValadonRasTop 1.3 August 2000© Philippe Valadon 2000
Herbert J. BernsteinRasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999
RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.5 June 2009
RasMol 2.7.5.1 July 2009
RasMol 2.7.5.2 May 2011
© Herbert J. Bernstein 1998-2009

RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakevand L. Andrews (via the neartree package). Work on RasMol 2.7.5supported in part by grant 1R15GM078077-01 from the National Instituteof General Medical Sciences (NIGMS), U.S. National Institutes of Healthand by grant ER63601-1021466-0009501 from the Office of Biological &Environmental Research (BER), Office of Science, U. S. Department ofEnergy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH andgrant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporateschanges by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Workon RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281and EF-0312612 from the U.S. National Science Foundation and grantDE-FG02-03ER63601 from BER/DOE. The content is solely the responsibilityof the authors and does not necessarily represent the official views ofthe funding organizations.

The code for use of RasMol under GTK in RasMol 2.7.4.2 was written byTeemu Ikonen.

and Incorporating Translations by
AuthorItemLanguage
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 ManualSpanish
José Miguel Fernández Fernández2.7.1 ManualSpanish
Fernando Gabriel Ranea2.7.1 menus and messagesSpanish
Jean-Pierre Demailly2.7.1 menus and messagesFrench
Giuseppe Martini, Giovanni Paolella,
A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov2.7.3 menus and messagesRussian
G. Todorov2.7.3 menus and messagesBulgarian
Nan Jia, G. Todorov2.7.3 menus and messagesChinese
Mamoru Yamanishi, Katajima Hajime2.7.3 menus and messagesJapanese
This Release by
Herbert J. Bernstein,Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright © Herbert J. Bernstein 1998-2009
Mac

The original RasMol manual was created by Roger Sayle. In July 1996,Dr. Margaret Wong of the Chemistry Department, Swinburne Universityof Technology, Australia, made extensive revisions to the RasMol 2.5manual to accurately reflect the operation of RasMol 2.6. Eric Martzof the University of Massachusetts made further revisions. In May1997, William McClure of Carnegie Mellon University reorganized theHTML version of the manual into multiple sections which could bedownloaded quickly and added use of frames. Portions of the 2.7.1version of the RasMol manual were derived with permission fromWilliam McClure's version using Roger Sayle's rasmol.doc forversion 2.6.4 as the primary source. Changes were made inAugust 2000 for RasMol version 2.7.2, January 2001 for RasMolversion 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 andFebruary 2005 for RasMol version 2.7.3.

Documentation Last Updated 14 May 2011
Edited by Herbert J. Bernstein and Frances C. Bernstein

Translations

Thanks to the efforts of José Miguel FernándezFernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada.España (jmfernan@ugr.es)) a translation of theManual for Rasmol version 2.7.1 into Spanish is now available.La traducción española del manual de laversión de la Dra. Wong revisada por Eric Martz fue realizada porIsabel Serván Martínez y José Miguel FernándezFernández. La actual traducción del Manual de RasMol 2.7.1ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández.

Rasmol Mac Os X Download Software

Thanks to translations by Fernando Gabriel Ranea in late 2000and early 2001, RasMol is nowcapable of rendering most menu items and messages in Spanish. Jean-Pierre Demailly provided Frenchtranslations of menus and messages in January 2001. Giuseppe Martini and Giovanni Paolella with contributions by A. Davassi, M. Masullo and C. Liotto provided Italiantranslations of menus and messages in March 2001.

IMPORTANT - Copying and Distribution

This version is based directly on RasMol version 2.7.5.1,on RasMol version 2.7.4.2,on RasMol version 2.7.4.1,on RasMol version 2.7.4,on RasMol version 2.7.3.1,on RasMol version 2.7.3, on RasMol version 2.7.2.1.1,on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMolversion 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version2.6.4, and RasMol 2.5-ucb and 2.6-ucb.

Please read the file NOTICE forimportant notices which apply to this package and forlicense terms (GPL or RASLIC).

Contents

  • Directories
    • ChangeLog -- Full ChangeLog directory
    • src -- source code
      • mac -- Macintosh build directory
      • mswin -- Windows build directory
    • doc -- documentation
    • data -- sample data files

Rasmol Mac Os X Download For Mac

Introduction

This posting is made to announce the release of RasMol version2.7.5.2 This release is based on RasMol 2.7.5.1.

This is a final update to the 2.7.5 series before release of the 2.7.6 releasecandidates, correcting some minor bugs and speeding up surface renderingsby use of NearTree 3.1. The version of CBFlib used has also been updated.The changes made between the 2.7.5.1 release of 23 July 2009 and the2.7.5.2 release were:

  • Faster surface rendering by use of NearTree 3.1
  • Updates to GTK version from T. Ikonen
  • Use of CBFlib 0.9.2
  • Use of CQRlib 1.1.2
  • Minor bug fixes

The changes made between the 2.7.5 release candidate release of 17 July 2009and the formal release on 23 July 2009 were:

Rasmol Mac Os X Download Full

  • Correction to the support for core CIF data file loads that was disabled in themove to CBFlib in place of the internal CIF support.
  • Correction to the CCP4 map read logic in the case of symmetrylines. Thanks to Marian Szebenyi for finding this bug.
  • Clarification to the install instructions for 64-bit unix systems.Thanks to Marian Szebenyi and Mark Diekhans for pointing out the lackof clarity.

The major changes from the 2.7.4.2 release to the 2.7.5 release include:

  • Support for SBEVSL movie commands.
  • Support for Lee-Richards surface approximation by contouring pseudo-Gaussianelectron densities.
  • Selection of atoms by proximity to map contours
  • Coloring of maps by the colors of neighboring atoms
  • Significant improvements to the GTK version by Teemu Ikonen
The 2.7.4.2 release was based on RasMol 2.7.4 and RasMol 2.7.4.1 andRasMol 2.7.3.1,the final reference release for the 2.7.3 series. The changes from the 2.7.3.1 release to the2.7.4.1 release included:
  • Support for maps.
  • Message and menu translations for Russian, Bulgarian, Japanese and Chinese.Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime.
  • Fix torsion angle calculation as per bug report and patch by Swati Jain.
  • Corrections by Ladislav Michnovic to port to more platforms.
  • Code to read remediated PDB entries as suggested by Huanwang Yang
  • Updated icons.
  • Extended export menus.
For more detail on these and earlier changes, consult the openrasmol svn repositoryon sourceforge.

This version is available for MS Windows and various unix-systems.As binaries become available, they will be released onhttp://blondie.dowling.edu/projects/rasmolandhttp:/www.sourceforge.net/projects/openrasmol.

For installation instructions see 'INSTALL'.

For a list of open issues in this version, see 'TODO'.

RasMol is a molecular graphics program intended for the visualisationof proteins, nucleic acids and small molecules. The program is aimed atdisplay, teaching and generation of publication quality images. The originalprogram was been developed at the University of Edinburgh'sBiocomputing Research Unit and the Biomolecular Structures Group atGlaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats andinteractively displays the molecule on the screen in a variety of colourschemes and representations. Currently supported input file formatsinclude Brookhaven Protein Databank (PDB), Tripos' Alchemy and SybylMol2 formats, Molecular Design Limited's (MDL) Mol file format,Minnesota Supercomputer Center's (MSC) XMol XYZ format, CHARMm format,MOPAC format, CIF format and mmCIF format files. If connectivityinformation and/or secondary structure information is not contained inthe file this is calculated automatically. The loaded molecule may beshown as wireframe, cylinder (drieding) stick bonds, alpha-carbontrace, spacefilling (CPK) spheres, macromolecular ribbons (eithersmooth shaded solid ribbons or parallel strands), hydrogen bonding anddot surface. Atoms may also be labelled with arbitrary text strings.Alternate conformers and multiple NMR models may be specially colouredand identified in atom labels. Different parts of the molecule may bedisplayed and coloured independently of the rest of the molecule orshown in different representations simultaneously. The space fillingspheres can even be shadowed. The displayed molecule may be rotated,translated, zoomed, z-clipped (slabbed) interactively using either themouse, the scroll bars, the command line or an attached dials box.RasMol can read a prepared list of commands from a `script' file (orvia interprocess communication) to allow a given image or viewpoint tobe restored quickly. RasMol can also create a script file containingthe commands required to regenerate the current image. Finally therendered image may be written out in a variety of formats includingboth raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfileor as a MolScript input script or Kinemage.

Versions of RasMol have run on a wide range of architectures and systems including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBMRS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBMPC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD),Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DECWindows). UNIX and VMS versions require an 8bit, 24bit or 32bit XWindows frame buffer (X11R4 or later). The X Windows version of RasMolprovides optional support for a hardware dials box and acceleratedshared memory rendering (via the XInput and MIT-SHM extensions) ifavailable.

Reports of builds and/or problems on various platforms appreciated.

Rasmol Mac Os X Download

Rasmol Mac Os X Download 10 11 4

Source Code and Binaries

The complete source codeand user documentation of RasMol 2.7.5.2 may be obtained http://www.sourceforge.net/projects/rasmol.andbyanonymous FTP at:

or on the web at:

http://www.sourceforge.net/projects/rasmol.