rasmol/rasmol
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
<!doctype html public "-//IETF//DTD HTML 2.0//EN"> <HTML> <HEAD> <TITLE> RasMol V2.7.5.2 README </TITLE> </HEAD> <BODY BACKGROUND="html_graphics/rasmolwallpaper.jpg"> <font face="Helvetica,Arial,Times" size=2> <a href="http://www.iucr.org/iucr-top/welcome.html"> <img alt="[IUCr Home Page]" src="html_graphics/iucrhome.jpg"></a> <a href="http://www.iucr.org/iucr-top/cif/home.html"> <img alt="[CIF Home Page]" src="html_graphics/cifhome.jpg"></a> <A HREF="doc/rasmol.html"><IMG SRC="html_graphics/rasmolbutton.jpg" ALT="[RasMol Manual]"></A> <hr> <CENTER> | <a href="http://www.OpenrasMol.org">OpenRasMol</a> | <A href="README.html#Copying">Copying and Distribution</A> | <A href="README.html#Contents">Contents</A> | <A href="INSTALL.html">Installation Instructions</A> |<BR> | <A href="ChangeLog.html">Changes</A> | <A href="TODO.html">Things To Do</A> | <A href="README.html#Introduction">Introduction</A> | <A href="README.html#CodeAndBinaries">Source Code and Binaries</A> |<BR> | <A href="doc/rasmol.html">RasMol Manual</A> | <a href="doc/esrasmol27.html">Spanish Translation of RasMol Manual</a> | <a href="doc/itrasmol.hlp">Italian Translation of RasMol Help File</a> |<BR> | <a href=http://www.rasmol.org/donate.shtml>Donate to Support RasMol</a> | <a href="README.html">Release README</A> | <a href=http://www.rasmol.org/register.shtml>Register your RasMol</a> | <br /> </CENTER> <font color="#0808A0"> <H1 ALIGN=CENTER>README<BR> RasMol 2.7.5.2</H1> <center> <table celpadding=0> <tr> <td valign=top bgcolor="#A0FFFF"><font face="Helvetica,Arial,Times" size=2> <ul> <li><a href=http://www.rasmol.org/software/RasMol_Latest_Windows_Installer.exe>RasMol Latest Windows Installer</a> <br /> <br /> <li><a href=http://www.rasmol.org/software/RasMol_Latest.tar.gz>RasMol Latest Source Tarball </a><br /> <br /> <li><a href=http://www.rasmol.org/software/RasMol_Latest_Manual.html>RasMol Latest Manual </a><br /> <br /> <li><a href=http://www.rasmol.org/donate.shtml>Donate to Support RasMol </a><br /> <li><a href=http://www.rasmol.org/register.shtml>Register your RasMol</a><br /> </ul> </font> <td> <td><IMG SRC="html_graphics/rasmollogo.jpg" ALT="RasMol"> <td> <td valign=top bgcolor="#FFFFA0"><font face="Helvetica,Arial,Times" size=2> <ul> <li><a href=http://www.rasmol.org/software/RasMol_2.7.5.2_Windows_Installer.exe>RasMol 2.7.5.2 Windows Installer</a> <br /> <br /> <li><a href=http://www.rasmol.org/software/RasMol_2.7.5.2.tar.gz>RasMol 2.7.5.2 Source Tarball</a><br /> <br /> <li><a href=http://www.rasmol.org/software/RasMol_2.7.5_Manual.html>RasMol 2.7.5 Manual</a><br /> <br /> <li><a href=http://www.rasmol.org/donate.shtml>Donate to Support RasMol </a><br /> <li><a href=http://www.rasmol.org/register.shtml>Register your RasMol</a><br /> </ul> </font> </table> </center> <H3 ALIGN=CENTER> Molecular Graphics Visualisation Tool<br /> 3 June 2009 (rev. 13 May 2011)<br /> </h3> </font><font color="#000000"> <CENTER> Based on RasMol 2.6 by Roger Sayle<br /> Biomolecular Structures Group, Glaxo Wellcome Research & Development, Stevenage, Hertfordshire, UK<br /> Version 2.6, August 1995, Version 2.6.4, December 1998<br /> Copyright © Roger Sayle 1992-1999 </CENTER> <P> <CENTER> and Based on Mods by <table border=3> <tr><th align="left">Author<th align="left">Version, Date<th align="left">Copyright <tr><td>Arne Mueller<td>RasMol 2.6x1 May 1998<td>© Arne Mueller 1998 <tr><td valign="top">Gary Grossman and<br>Marco Molinaro<td>RasMol 2.5-ucb November 1995<br>RasMol 2.6-ucb November 1996 <td valign="top">© UC Regents/ModularCHEM<br>Consortium 1995, 1996 <tr><td>Philippe Valadon<td>RasTop 1.3 August 2000<td>© Philippe Valadon 2000 <tr><td valign="top">Herbert J. Bernstein<td>RasMol 2.7.0 March 1999<br> RasMol 2.7.1 June 1999<br>RasMol 2.7.1.1 January 2001<br /> RasMol 2.7.2 August 2000<br> RasMol 2.7.2.1 April 2001<br> RasMol 2.7.2.1.1 January 2004<br /> RasMol 2.7.3 February 2005<br /> RasMol 2.7.3.1 Apr 06<br /> RasMol 2.7.4 Nov 07<br /> RasMol 2.7.4.1 Jan 08<br /> RasMol 2.7.4.2 Mar 08<br /> RasMol 2.7.5 June 2009<br /> RasMol 2.7.5.1 July 2009<br /> RasMol 2.7.5.2 May 2011<br /> <td valign="top">© Herbert J. Bernstein 1998-2009 </table> </CENTER> <P> RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported in part by grant 1R15GM078077-01 from the National Institute of General Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant ER63601-1021466-0009501 from the Office of Biological & Environmental Research (BER), Office of Science, U. S. Department of Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National Science Foundation and grant DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding organizations. <P> The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by Teemu Ikonen. <CENTER> and Incorporating Translations by <table border=3> <tr><th align="left">Author<th align="left">Item<th align="left">Language <tr><td>Isabel Serván Martínez,<br> José Miguel Fernández Fernández <td valign="top">2.6 Manual<td valign="top">Spanish <tr><td>José Miguel Fernández Fernández<td>2.7.1 Manual<td>Spanish <tr><td>Fernando Gabriel Ranea<td>2.7.1 menus and messages<td>Spanish <tr><td>Jean-Pierre Demailly<td>2.7.1 menus and messages<td>French <tr><td>Giuseppe Martini, Giovanni Paolella,<br>A. Davassi, M. Masullo, C. Liotto <td valign="top">2.7.1 menus and messages<br> 2.7.1 help file<td valign="top">Italian <tr><td>G. Pozhvanov<td valign="top">2.7.3 menus and messages<td>Russian <tr><td>G. Todorov<td valign="top">2.7.3 menus and messages<td>Bulgarian <tr><td>Nan Jia, G. Todorov<td valign="top">2.7.3 menus and messages<td>Chinese <tr><td>Mamoru Yamanishi, Katajima Hajime<td valign="top">2.7.3 menus and messages<td>Japanese <tr> <tr> </table> </CENTER> <P> <CENTER> This Release by <BR>Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA<BR> <script language="javascript" type="text/javascript"> <!-- var name = "yaya@"; var domain = "bernstein-plus-sons"; var domext = ".com"; document.write ("<a href=\"mailto:" + name + domain + domext + "\">" + name + domain + domext+"</a>"); // --> </script> <noscript> yaya@bernstein-plus-sons.com </noscript> <BR> Copyright © Herbert J. Bernstein 1998-2009<BR> </CENTER> <P> The original RasMol manual was created by Roger Sayle. In July 1996, Dr. Margaret Wong of the Chemistry Department, Swinburne University of Technology, Australia, made extensive revisions to the RasMol 2.5 manual to accurately reflect the operation of RasMol 2.6. Eric Martz of the University of Massachusetts made further revisions. In May 1997, William McClure of Carnegie Mellon University reorganized the HTML version of the manual into multiple sections which could be downloaded quickly and added use of frames. Portions of the 2.7.1 version of the RasMol manual were derived with permission from William McClure's version using Roger Sayle's rasmol.doc for version 2.6.4 as the primary source. Changes were made in August 2000 for RasMol version 2.7.2, January 2001 for RasMol version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and February 2005 for RasMol version 2.7.3. <p> <CENTER>Documentation Last Updated 14 May 2011<br> Edited by Herbert J. Bernstein and Frances C. Bernstein </CENTER> <p> <H4 Align="CENTER">Translations</H4> <P>Thanks to the efforts of José Miguel Fernández Fernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada. España (<A HREF="mailto:jmfernan@ugr.es">jmfernan@ugr.es</A>)) a <a href="doc/esrasmol27.html">translation of the Manual for Rasmol version 2.7.1 into Spanish</a> is now available. La traducción española del manual de la versión de la Dra. Wong revisada por Eric Martz fue realizada por Isabel Serván Martínez y José Miguel Fernández Fernández. La actual traducción del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández. <P> Thanks to translations by Fernando Gabriel Ranea <davinci@dinamica.com.ar> in late 2000 and early 2001, RasMol is now capable of rendering most menu items and messages in Spanish. Jean-Pierre Demailly <Jean-Pierre.Demailly@ujf-grenoble.fr> provided French translations of menus and messages in January 2001. Giuseppe Martini <martini@iigb.na.cnr.it> and Giovanni Paolella <paolella@dbbm.unina.it> with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian translations of menus and messages in March 2001. </P> <HR> <H2 ALIGN=CENTER><a name=Copying></a>IMPORTANT - Copying and Distribution</H2> <P> 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 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. <P> Please read the file <A HREF = "doc/NOTICE.html">NOTICE</A> for important notices which apply to this package and for license terms (<a href=GPL>GPL</a> or <A href=RASLIC>RASLIC</a>). <HR> <H3><A NAME="Contents">Contents</A></H3> <P> <UL> <LI><A href="#Copying">IMPORTANT - Copying and Distribution</A> <LI><A href="INSTALL.html">Installation Instructions</A> <LI><A href="ChangeLog.html">Changes</A> <LI><A href="TODO.html">Things To Do</A> <LI><A href="#Introduction">Introduction</A> <LI><A href="#CodeAndBinaries">Source Code and Binaries</A> <LI>Directories <UL> <LI><A href="ChangeLog/">ChangeLog</A> -- Full ChangeLog directory <LI><A href="src/">src</A> -- source code <UL> <LI><A href="src/mac/">mac</A> -- Macintosh build directory <LI><A href="src/mswin/">mswin</A> -- Windows build directory </UL> <LI><A href="doc/README.html">doc</A> -- documentation <LI><A href="data/">data</A> -- sample data files </UL> </UL> <HR> <H3 ALIGN=CENTER><A NAME="Introduction">Introduction</A></H3> <p>This posting is made to announce the release of RasMol version 2.7.5.2 This release is based on <a href="http://www.bernstein-plus-sons.com/software/RasMol_2.7.5">RasMol 2.7.5.1</a>. <p> This is a final update to the 2.7.5 series before release of the 2.7.6 release candidates, correcting some minor bugs and speeding up surface renderings by 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 the 2.7.5.2 release were: <p> <ul> <li>Faster surface rendering by use of NearTree 3.1</li> <li>Updates to GTK version from T. Ikonen <li>Use of CBFlib 0.9.2 <li>Use of CQRlib 1.1.2 <li>Minor bug fixes </ul> <p> The changes made between the 2.7.5 release candidate release of 17 July 2009 and the formal release on 23 July 2009 were: <ul> <li> Correction to the support for core CIF data file loads that was disabled in the move to CBFlib in place of the internal CIF support. <li> Correction to the CCP4 map read logic in the case of symmetry lines. Thanks to Marian Szebenyi for finding this bug. <li> Clarification to the install instructions for 64-bit unix systems. Thanks to Marian Szebenyi and Mark Diekhans for pointing out the lack of clarity. </ul> <p> The major changes from the 2.7.4.2 release to the 2.7.5 release include: <ul> <li> Support for SBEVSL movie commands. <li> Support for Lee-Richards surface approximation by contouring pseudo-Gaussian electron densities. <li> Selection of atoms by proximity to map contours <li> Coloring of maps by the colors of neighboring atoms <li> Significant improvements to the GTK version by Teemu Ikonen </ul> The 2.7.4.2 release was based on RasMol 2.7.4 and RasMol 2.7.4.1 and <a href="http://www.bernstein-plus-sons.com/software/RasMol_2.7.3.1">RasMol 2.7.3.1</a>, the final reference release for the 2.7.3 series. The changes from the 2.7.3.1 release to the 2.7.4.1 release included: <ul> <li> Support for maps. <li> Message and menu translations for Russian, Bulgarian, Japanese and Chinese. Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime. <li> Fix torsion angle calculation as per bug report and patch by Swati Jain. <li> Corrections by Ladislav Michnovic to port to more platforms. <li> Code to read remediated PDB entries as suggested by Huanwang Yang <li> Updated icons. <li> Extended export menus. </ul> For more detail on these and earlier changes, consult the openrasmol svn repository on sourceforge. <P> This version is available for MS Windows and various unix-systems. As binaries become available, they will be released on <a href=http://blondie.dowling.edu/projects/rasmol>http://blondie.dowling.edu/projects/rasmol</a> and <a href=http://www.sourceforge.net/projects/openrasmol>http:/www.sourceforge.net/projects/openrasmol</a>. <P> For installation instructions see <A href="INSTALL.html">"INSTALL"</A>. <P> For a list of open issues in this version, see <A href="TODO.html">"TODO"</A>. <P> RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The original program was been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK. <P> RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 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 connectivity information and/or secondary structure information is not contained in the file this is calculated automatically. The loaded molecule may be shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. Atoms may also be labelled with arbitrary text strings. Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be displayed and coloured independently of the rest of the molecule or shown in different representations simultaneously. The space filling spheres can even be shadowed. The displayed molecule may be rotated, translated, zoomed, z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dials box. RasMol can read a prepared list of commands from a `script' file (or via interprocess communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally the rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage. <P> 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, IBM RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available. <P> Reports of builds and/or problems on various platforms appreciated. <P> <HR> <H3 ALIGN=CENTER><A NAME="CodeAndBinaries">Source Code and Binaries</A></H3> <P> The complete source code and user documentation of RasMol 2.7.5.2 may be obtained <a href=http://www.sourceforge.net/projects/openrasmol>http://www.sourceforge.net/projects/rasmol</a>. and by anonymous FTP at: <P> <A href="ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz">ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz</A> <P> or on the web at: <P> <A href="http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz">http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz</A> <P> <a href=http://www.sourceforge.net/projects/openrasmol>http://www.sourceforge.net/projects/rasmol</a>. <P> <center> <P> Any comments, suggestions or questions about this modified version of RasMol should be directed to <A HREF="mailto:rasmol@bernstein-plus-sons.com">rasmol@bernstein-plus-sons.com</A>. <P> <CENTER> | <a href="http://www.OpenrasMol.org">OpenRasMol</a> | <A href="README.html#Copying">Copying and Distribution</A> | <A href="README.html#Contents">Contents</A> | <A href="INSTALL.html">Installation Instructions</A> |<BR> | <A href="ChangeLog.html">Changes</A> | <A href="TODO.html">Things To Do</A> | <A href="README.html#Introduction">Introduction</A> | <A href="README.html#CodeAndBinaries">Source Code and Binaries</A> |<BR> | <A href="doc/rasmol.html">RasMol Manual</A> | <a href="doc/esrasmol27.html">Spanish Translation of RasMol Manual</a> | <a href="doc/itrasmol.hlp">Italian Translation of RasMol 2.7.1 Help File</a> |<BR> | <a href=http://www.rasmol.org/donate.shtml>Donate to Support RasMol</a> | <a href="README.html">Release README</A> | <a href=http://www.rasmol.org/register.shtml>Register your RasMol</a> | </CENTER> <HR> Updated 14 May 2011.<BR> Herbert J. Bernstein<BR> Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA<BR> <script language="javascript" type="text/javascript"> <!-- var name = "yaya@"; var domain = "bernstein-plus-sons"; var domext = ".com"; document.write ("<a href=\"mailto:" + name + domain + domext + "\">" + name + domain + domext+"</a>"); // --> </script> <noscript> yaya@bernstein-plus-sons.com </noscript> </font> </BODY> </HTML>
About
Community repository for open source rasmol
Resources
Stars
Watchers
Forks
Packages 0
No packages published