RasMol V2.7.5.2 README

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# README
RasMol 2.7.5.2

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### Molecular Graphics Visualisation Tool
3 June 2009 (rev. 13 May 2011)

Based on RasMol 2.6 by Roger 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

Author | Version, Date | Copyright
--- | --- | ---
Arne Mueller | RasMol 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 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 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. 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.

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

and Incorporating Translations by

Author | Item | Language
--- | --- | ---
Isabel Serván Martínez, José Miguel Fernández Fernández | 2.6 Manual | Spanish
José Miguel Fernández Fernández | 2.7.1 Manual | Spanish
Fernando Gabriel Ranea | 2.7.1 menus and messages | Spanish
Jean-Pierre Demailly | 2.7.1 menus and messages | French
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto | 2.7.1 menus and messages 2.7.1 help file | Italian
G. Pozhvanov | 2.7.3 menus and messages | Russian
G. Todorov | 2.7.3 menus and messages | Bulgarian
Nan Jia, G. Todorov | 2.7.3 menus and messages | Chinese
Mamoru Yamanishi, Katajima Hajime | 2.7.3 menus and messages | Japanese

This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
Copyright © Herbert J. Bernstein 1998-2009

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.

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

#### Translations

Thanks to the efforts of José Miguel Fernández Fernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada. España (jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1 into Spanish 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.

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

### Contents

- IMPORTANT - Copying and Distribution
- Installation Instructions
- Changes
- Things To Do
- Introduction
- Source Code and Binaries
- 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 release of RasMol version 2.7.5.2 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 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:

- 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 2009 and the formal release on 23 July 2009 were:

- 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.
- Correction to the CCP4 map read logic in the case of symmetry lines. 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 lack of 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-Gaussian electron 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 and RasMol 2.7.3.1, 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:

- 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 repository on sourceforge.

This version is available for MS Windows and various unix-systems. As binaries become available, they will be released on http://blondie.dowling.edu/projects/rasmol and http:/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 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.

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.

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.

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

### Source Code and Binaries

The complete source code and user documentation of RasMol 2.7.5.2 may be obtained http://www.sourceforge.net/projects/rasmol. and by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz

or on the web at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz

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

Any comments, suggestions or questions about this modified version of RasMol should be directed to rasmol@bernstein-plus-sons.com.

| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of RasMol 2.7.1 Help File |
| Donate to Support RasMol | Release README | Register your RasMol |

Updated 14 May 2011.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA