RasMol and OpenRasMol (original) (raw)

RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol. The site itself is provided courtesy of Bernstein + Sons. Maintenance of RasMol, much of the development, and integration of modifications provided by the community is done at the ARCiB project at RIT. For the convenience of contributors to the RasMol project, an open source collaborative development site is used:

http://www.sourceforge.net/projects/openrasmol
is the external development site provided by SourceForge, Inc.

Members of the community are welcome to join us on the site.

Work on RasMol has been supported in part by grants from the U.S. Department of Energy, the U.S. National Science Foundation and the U.S. NIH National Institute of General Medical Sciences. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies.

User support in the form of donations will help us to continue the development of RasMol. Registration will help us to keep you posted on new versions.

In order to ensure continuing availability of source code and documentation most programs and documents on this site are subject to copyright. This does not prevent you from using the open-source versions of RasMol, from making copies and changes, but prevents the creation of "closed source" versions out of the open source versions. Appropriate copyrights and licenses appear with the relevant sources and documents. SeeCopyright and NOTICEfor applicable Copyright and other Notices.

Introduction

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. RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Science is best served when the tools we use are fully understood by those who wield those tools and by those who make used of results obtained with those tools. When a scientific tool exists as software, access to source code is an important element in achieving full understanding of that tool. As our field evolves and new versions of software are required, access to source allows us to adapt our tools quickly and effectively.

There has always been free access to the source of the main line of RasMol development. With the creation of the RasMol 2.7 series of releases starting in 1999, RasMol formally became an open source program. There is some confusion about the meaning of the phrase "open source". In the early days of software development, most scientific software source code was freely and openly shared with a minimum of formalities. These days, it appears that carefully drawn legal documents are necessary to protect free access to the source code of scientific software. We are all deeply indebted to Richard Stallman for showing us how a creative combination of copyrights and seemingly restrictive licenses could give us truly unfettered freedom to use programs, to read their source code and to develop new versions. TheGNU project, and the Linux project have shown that an open source approach works. Until the RasMol 2.7.3 release, we had not used the GNU General Public License (the "GPL") for OpenRasMol in the past, but the OpenRasMol conditions for use have correctly been called "GPL-like" and starting with RasMol 2.7.3, RasMol may now be distributed under the GPL. In view of the increasing used of GPL'd packages to support new features in RasMol, it is best to use the GPL for all versions from RasMol 2.7.3 onwards. This is certainly the case for binary releases from RasMol 2.7.5 onwards.

You can find a complete explanation of the OpenRasMol conditions for relases prior to the 2.7.3 release (RASLIC) in the page on Copying and Distribution. If you are a user of OpenRasMol programs, you will find that the copyrights and notices ask little more of you than that you avoid mistakes by others by keeping the notices with copies, display scientific integrity by citing your sources properly and treating this like other shared scientific developments by not inferring a warranty. If you are a software developer and wish to incorporate what you find here into new code, or to pick up bits and pieces and used them in another context, the situation becomes more complex. Read the copyrights and notices carefully. You will find that they are "infectious". Whatever you make from our Open Source code must itself be offered as Open Source code. In addition, in order to allow users to understand what has changed and to ensure orderly development you have to describe your changes.

To avoid any misunderstanding -- please note that when you contribute to RasMol by making changes and contributing code, you do notacquire a copyright in the program as a whole. We are delighted to acknowledge each author who contributes and to recognize their copyright from the moment of creation in their modifications, but once they make those modifications a part of RasMol to make what is called a "derived work" the resulting work is under the copyrights of Roger Sayle and Herbert Bernstein. This is necessary so that in the future we can have the option of ensuring that the open source licenses can be continued by transferring the copyright to another organization.

**IMPORTANT NOTE:**Future releases of RasMol will continue to offer the GPL and RASLIC as alternative licenses for the source code, but, in order to conform to the license conditions of various libraries to which executables may be linked, starting with RasMol 2.7.5 release, the GPL is the only valid license to use the binary distributions.

There is a lot still to be done before this site is fully functional. Many links and features need to be added. With your help, with your comments, suggestions and corrections, and with contributions of new Open Source RasMol code and documentation, hopefully this site will evolve into an increasingly useful tool for the community.

-- H. J. Bernstein

Software Distributions

RasMol Features

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. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.

The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. 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 represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box. RasMol can read a prepared list of commands from a 'script' file (or via inter-process 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 either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.

The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Please type "help notices" for important notices.

Released by R. Sayle (RasMol 2.1) 1993

RasMol 2.7.1 Features

The release of RasMol version 2.7.1 made 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 centring logic.

Released by H. J. Bernstein, 22 June 1999

RasMol 2.7.1.1 Features

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. Our thanks to Fernando Gabriel Ranea for most of the translations.
Upgrade of some of the Windows printer logic
Correction of coordinate handling for Mol2 and XYZ coordinates
Fix to the parsing of D2O.

Released by H. J. Bernstein, 21 January 2001

RasMol 2.7.2 Features

The preliminary release of RasMol 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 cooperation in contributing the UCB Enhanced RasMol code for incorporation into the RasMol 2.7 series.
Code to represent bonds in and to alternate conformers with a narrowed portion in the middle of each bond.
An attempt to fix some of the chirality reversals in some of the output modes.
Fixes for some of the problems reported since the last release.

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

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

RasMol may have difficulty in allocating colours for molecules after the first. The fix for this interacts with some other pending changes, and should be ready for the next release.
As has been true for all recent versions, the stereo mode defaults to cross-eyed, which is inconvenient for many users. The next release will 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 have not been incorporated into RasMol 2.7.2 yet. Our apologies. If you previously 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.

Released by H. J. Bernstein, 28 August 2000

RasMol 2.7.2.1 Features

The release of RasMol 2.7.2.1 made the following changes to RasMol 2.7.2, incorporating changes from RasMol 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 the problems in 2.7.2 and make the feel of 2.7.2.1 closer 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 from RasTop 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.

This release should hopefully represent a move toward stability for the 2.7.2 versions. However, in order to allow for prompt release of the French and Italian versions, some pending corrections have not yet been integrated. Comments and suggestions appreciated.

Released by H. J. Bernstein, 14 April 2001

RasMol 2.7.2.1.1 Features

The 2.7.2.1.1 release is the final reference release for the 2.7.2 series prior to the creation of version 2.7.3. For most users there should be no operational changes from version 2.7.2.1, except for the correction to the loading of PDB exchange dictionary CIFS.

Note: Patches to command.c were included to fix the handling of load inline in the UCB multiple molecule environment. In addition conditional code controlled by STRICT was disabled to restore operation of load inline under windows. Thanks to Jan Reichert for pointing out these problems. Thanks to E. Martz for pointing out an error in the Spanish translation credits which has been corrected.

Released by H. J. Bernstein, 26 January 2004

RasMol 2.7.3 Features

The 2.7.3 release is the initial release of the 2.7.3 series. This release includes the base level of code for software rendering of Lee-Richards molecular surfaces, and is intended to provide a stable base for hardware-assisted rendering of molecule surfaces in future releases, and for other changes. Work on RasMol 2.7.3 has been 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 the U.S. Department of Energy. This release has been in alpha test since February 2005 and is believed to now be ready for beta test. There are major additional changes pending to be applied once this base level is stable, including further molecular surface code and code to apply crystallographic and non-crystallographic symmetry. This release may be distributed under the GPL.

This release is based on RasMol 2.7.2.1.1, the final reference release for the 2.7.2 series. The changes for the 2.7.3 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 ZRange and 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 xforms for GUI file open. xforms.patch. This patch needs the opens source xforms 1.0.90 library by Steve 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 patches are available at xforms/
Correction to molecule.c to correct input of xyz files. Thanks to 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 available as CPK. (Revised 16 Jan 2005 by HJB).
Correction to negative torsion angle monitors and to imprecise 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 of the 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 a new Molecular Surface menu item, and surface molecule andsurface solvent commands. Two other, related, major patches are pending that depend upon this one: code by P. Zhivkov to simulate surfaces 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 these command with off instead of 0.

Released by H. J. Bernstein, 6 February 2005

RasMol 2.7.4 Features

The major changes in RasMol 2.7.4 are:

Extended language support. Messages and menus in Bulgarian, Chinese, English, Italian, Japanese, Russian and Spanish are now supported on systems with appropriate fonts. Our thanks to Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime for the Russian, Bulgarian, Chinese and Japanese translations.
Support for maps. On systems with sufficient memory, RasMol now can read maps in CCP4 and CBF map formats and can write maps in CBF map format. Maps of density from pseudo-Gaussian atoms can be generated. Support is provided for generation of surfaces for SAXS bead models.
An MS windows installer was proposed by G. A. Pozhvanov, and reimplemented on the open source base of NSIS-2.21.
A unix installer script, rasmol_install.sh, and a matching script to select an appropropriate binary version to run under unix, rasmol_run.sh have been added by H. J. Bernstein
In response to a bug report from Steve Shaw (shaws at mail dot nih dot gov) at the NIH, two new options have been added for export of VRML images: "rotate" and "mirror".
write vrml mirror
will write a vrml file with all axes mirrored (x -> -x, y -> -y and z -> -z) and
write vrml rotate
will write a vrml file rotated 180 degrees around the x-axis (x - > x, y -> -y, z-> -z)
Code from 2003 by Vencislav Stanev to export Raster3D scripts from RasMol was integerated with this release, and support for ribbons was added.
In order to support builds on newer 64-bit unix systems, Nikolay Darakev added code to the build scripts to check the length of long integers and to adjust the builds.
Other Corrections and improvements:
- 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.
- Alignment of command line sizing and positioning options for Windows and X-Windows version. The command line options -height nnnn, -width nnnn, -xpos nnnn and -ypos nnnn may be used to set the size and position of the initial window.
- Change of the encoding for Japanese messages and menus from SJIS to EUC-JP, and corrections to the fontset handling for Chinese and Japanese. Thanks to Mamoru Yamanishi for contributing the improved fontset logic.
- Updates to the rasmol_install.sh and rasmol_run.sh scripts to support Chinese and Japanese using cxterm.
- Optional use of GTK. Thanks to Teemu Ikonen for the new GTK code.

The svn at http://sf.net/projects/openrasmol should be consulted for details of the code changes.

Released by H. J. Bernstein 21 March 2008

RasMol 2.7.5 Features

This release is based on RasMol 2.7.4.2, the final reference release for the 2.7.4 series.

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 in RasMol 2.7.5 are:

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 SVN at http://sf.net/projects/openrasmol should be consulted for details of the code changes.

Released by H. J. Bernstein 17 July 2009

RasMol 2.7.2.1 zlib patches

The Unix version of RasMol supports decompression of compressed data files using pipes. Mamoru Yamanishi has prepared modifications for RasMol 2.7.2.1 to support use of decompression using the zlib (http://www.gzip.org/zlib) library, which should allow decompression of compressed data files on non-Unix platforms. These new modifications are being studied for inclusion in a future RasMol standard release for use on systems for which a pipe to a standard decompression utility is not practical to use. The source code mods to RasMol 2.7.2.1 for use of zlib under Mac OS are available for testing.

Released by Mamoru Yamanishi 13 July 2001

RasTop 1.3 Features

RasTop is a graphical interface to RasMol adapted for Windows platform, i.e. RasTop is a GUI front end for RasWin.

RasTop offers a user-friendly graphical interface around "RasMol molecular engine". No more typing on the command line; each command in the menu generates its own script that is transferred to RasMol. RasTop has numerous extensions to handle atom selections: addition and subtraction of atoms, groups, or chains, selection on screen with a lasso, ability to go back to the previous selection, copying to and pasting selections from the clipboard, new set operations such as inverse, extraction, summation, subtraction, and exclusion, and finally full saving of all user-defined atom sets under an extended script format called RSM script.

During its development, a few new capabilities were added: back clipping, 32-bit output under Windows, full centring command either on a selected atom or to the origin, variation of depthcue in slab mode, and a colouring command, shadepower, which generates new metal-like surfaces.

RasTop allows several molecules to be opened at the same time (on different windows) and provides limited editing of the molecular file.

RasTop 1.3, like RasMol 2.7.1, contains a lot of new code. Under its current version, RasTop 1.3 has been extensively tested with molecular files in pdb format and showed good stability. Nevertheless you should be careful in testing other formats.

Released by P. Valadon, 27 August 2000

RasTop 1.3.1 Features

This is a minor update with modifications concerning mainly correction of bugs reported for the 1.3 version. The software is now supported under Windows 2000 operating system. The software seems also stable under Windows ME. A release for 8-bit monitors is also available (although never tested on a true 256 colors monitor). A few systems are missing an updated version of the mfc42.dll file which is also available, but requires separate installation.

Operationally, there are very few changes. Maybe the most interesting for rasmol is the use of white color for carbon atoms when there are no hydrogen on the molecule on opening. The squareroot calculations for drawing ribbons at large zoom have been corrected.

Released by P. Valadon, 25 March 2001

RasTop 2.0 Features

RasTop 2.0 is a user-friendly graphical interface build on top of RasMol (version 2.7.2.1) available for Windows platforms. This is a major update over the 1.3.1 version. The interface now accepts multiple molecules. It has high color resolution and improvement of the rendering (depth queuing, multidirectional headlight, new cylinder code, better ribbons). The Richards - Connolly surfaces are now complete. A script can be started automatically on molecule opening.

Comments, suggestions, and bug reports will be extremely appreciated. The immediate goal is to obtain stable multiple molecule environment and compatibility with recent versions of Windows.

Released by P. Valadon, 20 January 2002

RasTop 2.1 Features

RasTop 2.1 is a user-friendly graphical interface build on top of RasMol available for Windows platforms.

In the RasTop 2.1 release "numerous bugs have been corrected ... A command window similar to the one in the original RasMol program has been added. This feature was requested by numerous teachers and was initially developed by Christian Duque. RasTop is now localizable to multiple languages, see RasTop help. A 'scripting' toolbar has been added to improve the handling of scripts. Scripts located in the "rastop/scripts" folder are directly accessible on the new toolbar. Images can be saved as bmp files in 32-bit format.

Released by P. Valadon, 14 September 2004

www.OpenRasMol.org

The OpenRasMol site is provided courtesy of Bernstein + Sons, Information Systems Consultants.

Portions © Copyright Herbert J. Bernstein 2000 -- 2006. All Rights Reserved. Other copyrights apply. License to copy most pages on this site will be granted if certain open source and other conditions are adhered to. See http://www.OpenRasMol.org/Copyright.html. To request permission to copy any elements from our pages, or to send comments about our pages, please write to If you establish a link to one of our pages, please let us know! Updated 24 July 2009