Mac OS X 10.10.1 Yosemite Free Download. Overview and Screenshots. Mac OS X Yosemite 10.10 is another product in Apple's line of Mac OS X titles. Mac OS X Yosemite 10.10.5 desktop. Yosemite includes various improvements over previous versions, one of the most prominent being the introduction of FaceTime, which is part of the Continuitypackage. $ begingroup$ 'I always use RasMol, to give visitors an idea of the kinds of pictures that they can create'. Oh no they can't! Rasmol does not run on Mac OS X. But you can use Jmol instead, which has a command for saving high res png files that you can actually drag back into the application and modify further.
visits since 28 Sep 2000 |
www.RasMol.org and www.OpenRasMol.org
| RasMol Manual |RasMol Blog |Frequently Asked Questions |RasMol 2.7 Series History |RasMol and OpenRasMol |
| SourceForge OpenRasMolSite |Click Here to Make a Donation |RasMol SourceForge Site |
Molecular Graphics Visualisation Tool
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RasMol is a program for molecular graphics visualisation originallydeveloped by Roger Sayle. This site is provided for the convenienceof 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 integrationof modifications provided by the community is done at theARCiB project at RIT. For the convenience ofcontributors to the RasMol project, an open source collaborativedevelopment 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 tocontinue the development of RasMol. Registration will help us to keep you postedon new versions.
In order to ensure continuing availability of source code anddocumentation most programs and documents on this siteare subject to copyright. This does not prevent you from usingthe open-source versions of RasMol, from making copies and changes,but prevents the creation of 'closed source' versionsout of the open source versions. Appropriate copyrights and licensesappear with the relevant sources and documents. SeeCopyright and NOTICEfor applicable Copyright and other Notices.
Contents
Introduction
Welcome to the RasMol and OpenRasMol web site. This site was established inmid-September 2000 to provide a home for developers of Open Source versions ofRasMol. In May 2002, it also became a home page for users of RasMol. RasMol is an important scientific tool for visualisationof molecules created by Roger Sayle in 1992. RasMol is used byhundreds of thousands of users world-wide to view macromoleculesand to prepare publication-quality images. Science is best servedwhen the tools we use are fully understood by those who wield thosetools and by those who make used of results obtained with those tools.When a scientific tool exists as software, access to source code isan 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 lineof RasMol development. With the creation of the RasMol 2.7 seriesof 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 aminimum of formalities. These days, it appears that carefully drawnlegal documents are necessary to protect free access to the sourcecode of scientific software. We are all deeply indebted to Richard Stallman for showingus how a creative combination of copyrights and seemingly restrictivelicenses 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 thatan 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 conditionsfor use have correctly been called 'GPL-like' and starting with RasMol 2.7.3, RasMol may now be distributedunder the GPL. In view of the increasing used of GPL'd packagesto support new features in RasMol, it is best to use the GPL forall versions from RasMol 2.7.3 onwards. This is certainly thecase 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 thatthe copyrights and notices ask little more of you than that youavoid mistakes by others by keeping the notices with copies,display scientific integrity by citing your sources properly andtreating this like other shared scientific developments by notinferring a warranty. If you are a software developer and wish to incorporate what youfind here into new code, or to pick up bits and pieces and used themin another context, the situation becomes more complex. Read thecopyrights and notices carefully. You will find that they are'infectious'. Whatever you make from our Open Source codemust itself be offered as Open Source code. In addition, inorder to allow users to understand what has changed and to ensure orderlydevelopment you have to describe your changes.
To avoid any misunderstanding -- please note that when you contribute toRasMol by making changes and contributing code, you do notacquire a copyright in the program as a whole. We are delighted toacknowledge each author who contributes and to recognize theircopyright from the moment of creation in their modifications, butonce they make those modifications a part of RasMol to make whatis called a 'derived work' the resulting work is under the copyrightsof Roger Sayle and Herbert Bernstein. This is necessary so thatin the future we can have the option of ensuring that the open sourcelicenses can be continued by transferring the copyright to anotherorganization.
IMPORTANT NOTE:Future releases of RasMol will continue tooffer the GPL and RASLIC as alternative licenses for the sourcecode, but, in order to conform to the license conditions ofvarious libraries to which executables may be linked, starting with RasMol 2.7.5 release, theGPL 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 toolfor the community.
Rasmol Program
Software Distributions
- RasMol -- latest test release (RasMol 2.7.5)
- RasMol -- current production release (RasMol 2.7.4.2)
- RasMol -- prior production release (RasMol 2.7.3.1)
- RasMol -- final 2.7.2 production release (RasMol 2.7.2.1.1)
- RasMol -- deprecated release (RasMol 2.7.1.1)
- RasTop -- latest stable release (RasTop 2.1)
- RasTop -- prior releases
- RasTop 2.0 Features
RasMol Features
RasMol is a molecular graphics program intended for the visualisation ofproteins, nucleic acids and small molecules.The program is aimed at display, teaching and generation ofpublication quality images. RasMol runs on wide range of architecturesand operating systems including Microsoft Windows, AppleMacintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or32 bit colour X Windows display (X11R4 or later). The X Windows version ofRasMol provides optional support for a hardware dials box and acceleratedshared memory communication (via the XInput and MIT-SHM extensions)if available on the current X Server.
The program reads in amolecule coordinate file and interactively displays the molecule on thescreen in a variety of colour schemes and molecule representations. Currentlyavailable representations include depth-cued wireframes, 'Dreiding' sticks,spacefilling (CPK) spheres, ball and stick, solid and strand biomolecularribbons, atom labels and dot surfaces.
The X Windows version of RasMol provides optional support for ahardware dials box and accelerated shared memory communication (viathe XInput and MIT-SHM extensions) if available on the current X Server.
The program reads in molecular coordinate files and interactivelydisplays the molecule on the screen in a variety of representationsand colour schemes. Supported input file formats include ProteinData Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats,Molecular Design Limited's (MDL) Mol file format, MinnesotaSupercomputer Center's (MSC) XYZ (XMol) format, CHARMm format,CIF format and mmCIF format files. If connectivity information isnot contained in the file this is calculated automatically. Theloaded 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 parallelstrands), hydrogen bonding and dot surface representations. Atomsmay also be labelled with arbitrary text strings. Alternate conformersand multiple NMR models may be specially coloured and identified inatom labels. Different parts of the molecule may be represented andcoloured independently of the rest of the molecule or displayed inseveral representations simultaneously. The displayed molecule maybe rotated, translated, zoomed and z-clipped (slabbed) interactivelyusing either the mouse, the scroll bars, the command line or an attacheddial box. RasMol can read a prepared list of commands from a 'script'file (or via inter-process communication) to allow a given image orviewpoint to be restored quickly. RasMol can also create a script filecontaining the commands required to regenerate the current image. Finally,the rendered image may be written out in a variety of formats includingeither raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfileor as a MolScript input script or Kinemage.
The RasMol help facility can be accessed by typing 'help <topic>' or 'help<topic> <subtopic>' from the command line. A complete list of RasMol commandsmay be displayed by typing 'help commands'. A single question mark may alsobe used to abbreviate the keyword 'help'. Please type 'help notices' forimportant notices.
Released by R. Sayle (RasMol 2.1) 1993
RasMol 2.7.1 Features
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 centring logic.
Released by H. J. Bernstein, 22 June 1999
RasMol 2.7.1.1 Features
The release of RasMol version 2.7.1.1made 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. Ourthanks 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 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 colours 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.
Released by H. J. Bernstein, 28 August 2000
RasMol 2.7.2.1 Features
The release of RasMol 2.7.2.1made 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.
This release should hopefully represent a move toward stability forthe 2.7.2 versions. However, in order to allow for prompt release of theFrench and Italian versions, some pending corrections have not yet beenintegrated. 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 jr@imb-jena.de for pointing out these problems. Thanks to E. Martz emartz@microbio.umass.edufor 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 releaseincludes 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 ofmolecule 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 appliedonce this base level is stable, including further molecular surface code andcode to apply crystallographic and non-crystallographic symmetry. This releasemay 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 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.
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. Messagesand menus in Bulgarian, Chinese, English, Italian, Japanese, Russian and Spanishare now supported on systems with appropriate fonts. Our thanks toOur thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajimefor the Russian, Bulgarian, Chinese and Japanese translations.
- Support for maps. On systems with sufficient memory, RasMol now canread maps in CCP4 and CBF map formats and can write maps in CBF mapformat. 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 reimplementedon the open source base of NSIS-2.21.
- A unix installer script, rasmol_install.sh, and a matching scriptto select an appropropriate binary version to run under unix, rasmol_run.shhave 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 newoptions have been added for export of VRML images: 'rotate'and 'mirror'.
write vrml mirror <filename>
will write a vrml file with all axes mirrored (x -> -x, y -> -yand z -> -z) and
write vrml rotate <filename>
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 scriptsfrom RasMol was integerated with this release, and support forribbons was added.
- In order to support builds on newer 64-bit unix systems, NikolayDarakev added code to the build scripts to check the length oflong 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 ofthe code changes.
Released by H. J. Bernstein 21 March 2008
Mac Os X Download Iso
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 2009and the formal release on 23 July 2009 were:
- 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 in RasMol 2.7.5 are:
- 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
Rasmol App
The SVN at http://sf.net/projects/openrasmol should be consulted for details ofthe 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 supportuse of decompression using the zlib (http://www.gzip.org/zlib) library, whichshould allow decompression of compressed data files on non-Unix platforms.These new modifications are being studied for inclusion in a future RasMolstandard 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 myamanishi3@unl.org,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 depthcuein 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 256colors 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 moleculeon 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 updateover the 1.3.1 version. The interface now accepts multiple molecules. It hashigh color resolution and improvement of the rendering (depth queuing,multidirectional headlight, new cylinder code, better ribbons). TheRichards - Connolly surfaces are now complete. A script can be startedautomatically on molecule opening.
Comments, suggestions, and bug reports will be extremely appreciated. Theimmediate goal is to obtain stable multiple molecule environment andcompatibility 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 RasMolavailable 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
| RasMol Manual |Frequently Asked Questions |RasMol 2.7 Series History |RasMol and OpenRasMol |
| Click Here to Make a Donation |
www.OpenRasMol.org
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
| 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 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 | © Herbert J. Bernstein 1998-2008 |
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| 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 |
Herbert J. Bernstein,Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
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 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.
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
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
IMPORTANT - Copying and Distribution
This version is based directly 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 vesion 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).
Obtaining RasMol v2.7.5
In order to install RasMol, you may start with a compiled binary or work from the source code.
The complete source codeand user documentation of RasMol 2.7.5 may be obtained from http://blondie.dowling.edu/projects/rasmolandhttp://blondie.dowling.edu/projects/rasmol.andbyanonymous FTP at:
or on the web at:
As compiled version become available, they will be posted at http://blondie.dowling.edu/projects/rasmolandhttp://blondie.dowling.edu/projects/rasmol.
To transfer by anonymous ftp, type 'ftp ftp.bernstein-plus-sons.com' on the commandline. Several seconds later you'll be prompted for a username. Use theusername 'anonymous' and when asked for a password enter your e-mailaddress. Once logged in, type the command 'cd software/rasmol' to changethe directory to /software/rasmol and then type 'binary' to avoid corruptingthe files during the transfer. For each file you wish to transfer, type'get <filename>' and when you've finished type 'quit'. If these files are subsequently transfered to other machines, please remember totransfer them in BINARY mode. The file sizes should be identical beforeand after the transfer.
NOTE: The Mac uses the 'carriage return' character to signify theend of a line, while UNIX machines use a 'linefeed'. If a file istransfered between these two machines in 'ASCII' mode all suchcharacters are exchanged, thereby corrupting the archive. Pleaseensure that you type the FTP command 'binary' before you transfer thefile, indicating that the file should be transfered withouttranslation.
If you wish to start from source code, you will need a RasMol source kit, andyou may need one or more external packages that are not part of RasMol, but whichare used by RasMol.
To build/rebuild RasMol 2.7.5 on any platform, you'll need to transfer the following file:
| RasMol.tar.gz | UNIX 'tar'ed 'gzip'ped archive containing the complete source code and documentation of the RasMol molecular graphics package. |
To unpack the file on a UNIX machine type the command 'gunzipRasMol.tar.gz' and then the command 'tar -xvfRasMol.tar' to extract the files in a subdirectory under thecurrent directory.
You will either need to have the following packages installed in your system, orto ensure that the indicated defines are at the start Imakefile:
- http://downloads.sf.net/neartree/NearTree-2.1.3.tar.gz or
#define NEARTREE_LOCAL - http://downloads.sf.net/cqrlib/CQRlib-1.0.3.tar.gz or
#define CQRLIB_LOCALhttp://http://downloads.sf.net/cvector/CVector-1.0.3.tar.gz or
#define CVECTOR_LOCAL - http://download.savannah.gnu.org/releases-noredirect/xforms/xforms-1.0.91.tar.gz or
#define XFORMSLIB_LOCAL - http://downloads.sf.net/cbflib/CBFlib-0.8.1.tar.gz or
#define CBFLIB_LOCAL
In addition, depending on what has already been installed on your system,you may need one or more of certain font kits. These packages are not partof RasMol and normally whould be obtained from their primary web sites, but,for convenience in installing RasMol, they have been gathered in theexternal_packages module in the CVS and as the External_Packages release on http://blondie.dowling.edu/projects/rasmolandhttp://www.sourceforge.net/projects/openrasmol.
These font kits are snapshots of the versions in use at the timeof the build of RasMol 2.7.5. The primary developer website for each package should be consulted for the latestversions. Because these kits may not be the same as later,standard versions that are used by the system, as a whole,scripts in RasMol that use thses kits (especially font kits)assume that each kit has been unpacked to a directory _within_the RasMol build directory, at the same level as the srcdirectory.
For RasMol release 2.7.5 the package snapshots other than the font kits have been replaced by the tableof downloads listed above.
For building for MS Windows, do not try to use Visual Studio. Use MINGW instead.
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.
On an SGI, rename the appropriate binary as rasmol and copy it to/usr/local/bin/rasmol (or to some appropriate location specifiedby the environment variable PATH) and copy rasmol.hlp to/usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by theenvironment variable RASMOLPATH)
Installing RasMol v2.7.5
UNIX X11:
If you are using a precompiled binary, see the instructions that are providedwith the binary kit. In general, the binary kits for unix provided directlyby this project are tarballs of the $HOME/lib/RasMol_2_7_5 created byrunning the script in src/rasmol_install.sh. The MS windows kit isa NSIS installer to be double-clicked after downloading.
- Fonts: Followling the instructions for your system, install whateverX11 font packages you need to the language variants of RasMol you intend touse. Almost all Unix variants come with the appropriate fonts for English,French, Spanish and Italian. There is an appropriate cyrillic font package,cyr-rfx-windows-1251-1.1, in external_packages. The Chinese and Japanesefonts in intlfonts-1.2.1.tar.gz in external_pakages seem to be satisfactory.
- In the RasMol src directory, either
Note for 64 bit CPUs: If you are building RasMol for a 64-bit CPUwith a compiler that has a 64-bit long data type, you must either usethe build_all.sh script, or manually
#define _LONGLONG
in rasmol.h
- Modify the #defines in the file rasmol.h (see below) Note: IBMPC should not be defined.
- either
- Use the script rasmol_build_options.sh to build a new Imakefilefrom Imakefile_base. The valid options are:
{--help|-h}
{--cbflib_local}
{--cqrlib_local}
{--cvector_local}
{--neartree_local}
{--xformslib_local}
{--use_xformslib}
{--use_gtk}
{--pixeldepth=32}
{--pixeldepth=16}
{--pixeldepth=8}
{--macosx_fink}or
- Edit Imakefile to change the desired options by hand. Use of rasmol_build_options.sh is in general perferred
- Use the script rasmol_build_options.sh to build a new Imakefilefrom Imakefile_base. The valid options are:
- either
- execute
&npsp;xmkmf
and - execute
&npsp;make rasmol
- edit the script build_all.sh
- execute build_all.sh
- execute
- A common problem is that SUN OpenWindows keeps its include files in the directory /usr/openwin/include/X11, hence the compiler directive -I/usr/openwin/include must be added to CFLAGS.
- A common problem on IBM RS6000s running AIX is that the MIT shared memory extensions to X windows are in the library -lXextSam, hence this must be added to the LIBS lines in either the Makefile or Imakefile.
MS Windows:
If you are using a precompiled binary, follow the instructions that comewith the binary, but in general, you either need to place raswin.exe,rasmol.hlp and raswin.hlp into the directory from which you will run,or you need to execute the installer program by double clicking it.
If you are building from source, you will need MINGW, not visual studio.CodeWarrior version 9 can also be used.
Macintosh under OSX:
Follow the instructions for unix and run under the X11 system. A pre-editedversion of the build_all.sh script called build_MACOSX.sh is provided.
COMPILATION DIRECTIVES
The file rasmol.h contains a number of #define directives that controlthe runtime behaviour of the program. The following directives may bedefined or undefined to suite the local site.
| THIRTYTWOBIT SIXTEENBIT EIGHTBIT | This determines whether RasMol will display and produce 8bit, 16bit or 32(24) bit output. By default the symbol EIGHTBIT is defined producing images with up to 256 colours. This symbol must be defined if IBMPC is defined. |
| DIALBOX | This enables the use of a dials box, that is connected using the X Window System XInput extension. This option requires that the program be compiled with the Xi and Xext libraries. Note: libXi is called libXinput on some old machines, so requires the compiler option -lXinput! |
| MITSHM | This option enables the use of the X Window System MIT shared memory extension. This enables images to be displayed faster when RasMol and the X11 server are running on the same host. This option requires the program be compiled with the Xext library. On IBM RS6000s runnning AIX, MITSHM also requires the XextSam library (which requires changing the Makefile or Imakefile). This is now enabled by default. This should be disabled on E&S ESV workstations as MITSHM support is not provided as standard. |
| TERMIOS | This directive enables the command line processing on UNIXs that support the termios terminal handling routines. By leaving this symbol undefined, RasMol omits the interactive command line interface. Undefining is not recommended! |
| SOCKETS | This directive enables the TCP/IP server functionality of RasMol to be enable. This enables other software to connect to a running RasMol. This should be undefined on machines not supporting BSD-style TCP/IP sockets (such as VMS). |
| APPLEMAC | This determines whether the program is to run on an Apple Macintosh or PowerMac. By default, this option is disabled. The Macintosh code may be compiled to be either EIGHTTBIT or THIRTYTWOBIT and will generate images effectively. |
| IBMPC | This determines whether the program is intended to run on an IBM PC or compatible. By default, this option is disabled. |
| MSWIN | This determines whether the program is intended to run on an IBM PC or compatible under MS Windows. By default, this option is disabled. |
| PROFILE | Defining PROFILE enables code to profile RasMol execution. |
| XPROCARCH | Defining XPROCARCH enables code for raswin that gets detailed information about the operating system and processor |
| USE_UNAME | Defining USE_UNAME enables code for rasmol under X11 that gets detailed information about the operating system and processor. |
| USE_CBFLIB | Defining USE_CBFLIB enables code t that depends on CBFLIB for map reading and writing. |
To summarise;
Any comments, suggestions or questions about thismodified version should be directed to Herbert J. Bernstein atrasmol@bernstein-plus-sons.com.
| Changes |Things To Do |Introduction | Source Code and Binaries |
| RasMol Manual |Spanish Translation of RasMol Manual | Italian Translation of RasMol Help File |
| Donate to Support RasMol |Release README |Register your RasMol |
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com