| Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Release README |

# README
RasMol 2.7.1

###
Molecular Graphics Visualisation Tool
22 June 1999

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 Arne Mueller
Version 2.6x1, May 1998
Copyright © Arne Mueller 1998

Version 2.7.0, 2.7.1 Mods by Herbert J. Bernstein
Bernstein + Sons, P.O. Box 177, Bellport, NY, USA, yaya@bernstein-plus-sons.com
2.7.0 March 1999, 2.7.1 June 1999
Copyright © Herbert J. Bernstein 1998-1999

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.

Documentation Last Updated 5 July 1999
Edited by Herbert J. Bernstein and Frances C. Bernstein

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

## IMPORTANT - Copying and Distribution

This version is based on RasMol version 2.6_CIF.2, on RasMol version 2.6x1 and on RasMol version 2.6.4. Please read the file NOTICE for important notices which apply to this package. If you are not going to make changes to RasMol, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following:

- 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and
- 2. Please give credit where credit is due citing the version and original authors properly; and
- 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind.

If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following:

- 4. Please explain in your documentation how what you did differs from this version of RasMol; and
- 5. Please make your modified source code available.

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.

### 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 to announce the release of RasMol version 2.7.1, which makes 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 Haltiwanger for suggesting this change.
- The ability to use a proportionally spaced font and to draw labels with 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 a technically minor, but operationally critical upgrade to version 2.7.0, correcting a serious error in the selection logic introduced in the process of 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. This combined version allows selection by alternate conformers as well as by models, production of Ramachandran printer plots (as in F. Bernstein's fisipl), and access to A. Mueller's POVray output as POVray3 in addition to the existing POVray version 2 output. (POVray3 should not be used in 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 or atoms 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 Roger Sayle, dropping obsolete non-ANSI C options and providing speed improvments.

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

Rasmol version 2.6_CIF(Rev 1) was a minor update to RasMol version 2.6_CIF, which added support for alternate conformer 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, because of limitations in the memory management under MacOS, very large multiple NMR model datasets are not supported on the Mac or PowerMac at this 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's prior list of pending projects is in "PROJECTS".

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 program has 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.

RasMol will 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.

As of this writing (6 July 1999), this version has been built for Linuxppc, SGI, DEC OpenVMS, Mac and IBM PC under Windows 95. Reports of builds and/or problems on other platforms appreciated. Our thanks to David Atkinson at BU, Bob Sweet at BNL, Helen Berman at John Westbrook at Rutgers for access to computers used for some of the compilations for this release. Additional thanks to David Atkinson for contributing the compiled Alpha Dunix binaries.

### Source Code and Binaries

The complete source code and user documentation of RasMol 2.7.1 may be obtained by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz

or on the web at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz

The source code and documentation are stored in several files appropriate for the receiving operating system. Please read the "README" file in the distribution directory. See the table below for appropriate binaries. Mac and Windows binaries are no longer included on the tar. Unix and VMS users should retrieve the same file for source code and documentation, and one or more of the following pre-compiled binaries: WARNING: ALL binaries are gzipped!!!

System | Binary | Help Files
--- | --- | ---
SGI (IRIX 5.3): | RasMol.SGI/IRIX_5.3/rasmol_8BIT.gz | rasmol.hlp.gz
| RasMol.SGI/IRIX_5.3/rasmol_16BIT.gz | rasmol.hlp.gz
| RasMol.SGI/IRIX_5.3/rasmol_32BIT.gz | rasmol.hlp.gz
SGI (IRIX 6.4): | RasMol.SGI/IRIX_6.4/rasmol_8BIT.gz | rasmol.hlp.gz
| RasMol.SGI/IRIX_6.4/rasmol_16BIT.gz | rasmol.hlp.gz
| RasMol.SGI/IRIX_6.4/rasmol_32BIT.gz | rasmol.hlp.gz
Alpha (OpenVMS 7.1): | RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe.gz | rasmol.hlp.gz
| RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe.gz | rasmol.hlp.gz
| RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe.gz | rasmol.hlp.gz
Alpha (Dunix 4.0D): | RasMol.DEC/Dunix_4.0D/rasmol_8bit.gz | rasmol.hlp.gz
| RasMol.DEC/Dunix_4.0D/rasmol_32bit.gz | rasmol.hlp.gz
VAX (OpenVMS 6.2): | RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe.gz | rasmol.hlp.gz
| RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe.gz | rasmol.hlp.gz
| RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe.gz | rasmol.hlp.gz
Mac: | RasMac_FAT_8BIT.bin.gz | rasmol.hlp.gz
| RasMac_PPC_8BIT.bin.gz |
| RasMac_68K_8BIT.bin.gz |
| RasMac_FAT_32BIT.bin.gz |
| RasMac_PPC_32BIT.bin.gz |
| RasMac_68K_32BIT.bin.gz |
Windows: | RasWin.exe.gz | rasmol.hlp.gz, raswin.hlp.gz

For those who have difficulty downloading "gzipped" files, uncompressed files are available:

System | Binary | Help Files
--- | --- | ---
SGI (IRIX 5.3): | RasMol.SGI/IRIX_5.3/rasmol_8BIT | rasmol.hlp
| RasMol.SGI/IRIX_5.3/rasmol_16BIT | rasmol.hlp
| RasMol.SGI/IRIX_5.3/rasmol_32BIT | rasmol.hlp
SGI (IRIX 6.4): | RasMol.SGI/IRIX_6.4/rasmol_8BIT | rasmol.hlp
| RasMol.SGI/IRIX_6.4/rasmol_16BIT | rasmol.hlp
| RasMol.SGI/IRIX_6.4/rasmol_32BIT | rasmol.hlp
Alpha (OpenVMS 7.1): | RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe | rasmol.hlp
| RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe | rasmol.hlp
| RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe | rasmol.hlp
Alpha (Dunix 4.0D): | RasMol.DEC/Dunix_4.0D/rasmol_8bit | rasmol.hlp
| RasMol.DEC/Dunix_4.0D/rasmol_32bit | rasmol.hlp
VAX (OpenVMS 6.2): | RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe | rasmol.hlp
| RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe | rasmol.hlp
| RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe | rasmol.hlp
Mac: | RasMac_FAT_8BIT.bin | rasmol.hlp
| RasMac_PPC_8BIT.bin |
| RasMac_68K_8BIT.bin |
| RasMac_FAT_32BIT.bin |
| RasMac_PPC_32BIT.bin |
| RasMac_68K_32BIT.bin |
Windows: | RasWin.exe | rasmol.hlp, raswin.hlp

You will need both an appropriate binary and a copy of rasmol.hlp for each system, 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 that the file size is the same before and after transfer.

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

| Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries | | RasMol Manual | Release README |

Updated 15 July 1999.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
+1-516-286-1339