For OS X you can either download a binary program, or install it from source using fink and the Apple version of X11 (see the Pymol site for details). Do search for pymol tutorials on the web. When you are exporting pictures to use with your web pages we recommend using a white background. RasMol 2.7.5 incorporates changes by T. 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 ER4 from the Office of Biological & Environmental Research.
- Introduction
- Setup of RasMol and Netscape
- Instructions for RasMol
WHAT IS RASMOL?
Available for Windows, Macintosh, and UNIX platforms, RasMol is a free, interactive molecular-graphics viewer. The program reads in the 3-D coordinates for a molecule using the pdb file format. It displays the molecule in various representations and allows one to rotate the molecule interactively. RasMol-ucb allows simultaneous viewing of multiple molecules.
HOW TO OBTAIN RASMOL AND TO SETUP NETSCAPE TO USE IT.
- To Download RasMol V2.6 ucb:
The version of RasMol that we are using (RasMol-ucb) is the enhanced version developed by Marco Molinaro from the UC Regents/ModularCHEM Consortium. Be aware that this program is still in beta testing; thus, you may encounter bugs. It is based on the original RasMol that was developed by Roger Sayle at Glaxo, UK. (Reference: Roger A. Sayle and E. J. Milner-White, 'RasMol: Biomolecular graphics for all', Trends in Biochemical Science (TIBS), September 1995, Vol. 20, No. 9, p.374.)
- Download the PC Windows version of RasMol-ucb. To install the PC windows version, double click on the Rasmol2.exe installer program. It is a self-extracting program and the executable is RasWin. This version runs under Windows 3.1, Windows 95, and Windows NT.
- Download the MAC version of RasMol-ucb. To install the MAC version*, double-click on the Rasmol-mac.sea program. It is a BinHex’ed, self-extracting archive for the Mac and PowerMac.
*NOTE TO MAC USERS: To download RasMol correctly from the internet, you need to have either 'Stuffit' or 'Binhex' on your Macintosh. These are free software programs and are available on the ACN (Academic Computing Network) Macintosh network or from Aladdin Systems. If you have any questions about this, please see R. Frey.
- To set up Netscape to use RasMol-ucb:
- If using Netscape 4.0, go to Edit/Preferences. (If using an older version of Netscape, go to Options/General Preferences/Helpers (or Helper Applications).) A dialog box will appear.
- Create New Type of Navigator Application for RasMol: In category section on the dialog box’s left side, use the mouse to click on the word 'Application' under the category 'Navigator.' Use the mouse to click the 'New' button. Enter the following information in the text fields that appear (NOTE: The text fields MAY or MAY NOT be in this order!).
- Descripter: chemical/x-pdb
- MIME type: chemical/x-pdb
- Suffix (Mac) or File Extensions (PC): pdb
- Action: launch application: RasMac (RasWin) (Use 'Browse' or 'Choose' button to find RasMac/RasWin on your hard drive. When RasMac/RasWin is highlighted, press <enter> or click the 'Open' button. MAC Users: You will have to use the mouse to select the radio button named 'Application.'
- Click 'Ok' or press <return> to return to Netscape Navigator.
INSTRUCTIONS TO USE RASMOL:
- Basic Instructions (using the menus):
- To open a file: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a .pdb file). (RasMol should automatically start and load in the molecule.)
- To open multiple files (i.e., can view up to 5 molecules simultaneously): File/Open (for each file, without closing the previous files) from within RasMol. From within Netscape, just click on another RasMol viewable molecule.
- To select a molecule: Click on molecule name in the Molecules window (the secondary window)
- To close a file (a molecule): File/Close when the molecule is selected.
- Moving the molecule(s):
- <alt><SHIFT>and right-mouse button
- To change to different representations (i.e., CPK, stick, ribbon, etc.): Display/Stick
- To determine distances, angles, dihedral angles:
- Click on appropriate icon in the Molecules window (the secondary window)
- Click once on the appropriate number of individual atoms. (With angles, clicking on atoms must be in the appropriate order.)
- To rotate bond (Note: This changes the angle.):
- Click on rotate angle icon in the Molecules window (the secondary window)
- Click on 2 atoms
- Click on rotate angle icon in the Molecules window (the secondary window) again
- Click on 3rd atom
- Use mouse button to rotate
- To color molecule in different ways:
- To color by the protein-secondary structure: Colours/Structure
- a -helices: magenta
- b -sheets: yellow
- turns: pale blue
- all other residues: white
- To color by residue type (i.e., each type of residue is colored a specific color): Colours/Shapely
- To color by atom type (below are the default colors): Colours/CPK
- Carbon: gray
- Hydrogen: white
- Oxygen: red
- Nitrogen: blue
- Sulfur: yellow
- Iron: yellow
Action
PC
MAC
Left-mouse
button (Click & Hold)Mouse button (Click & Hold)
Translation
Right-mouse
button (Click & Hold)<OpenApple> and
mouse button Minitool partition wizard is it safe.Zoom
<alt><SHIFT> and
left-mouse button<SHIFT> and
mouse buttonZ-Rotation
<option><SHIFT> and
mouse button - Advanced RasMol Usage:
The command line may also be used to perform more advanced commands. To find the commands, look in the RasMol manual under Help (PC) or ð/Basic Instructions. Other helps, such as reference manuals and tutorials, are available on the Internet:
- http://www.curtin.edu.au/curtin/dept/biomed/teach/biochem/tutorials/GetStart.html
- http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/RasTut.html
- http://klaatu.oit.umass.edu/microbio/rasmol/distrib/rasman.htm
[Return to VSEPR]
Revised July 29, 1999
www.OpenRasMol.org/FAQ.html
| RasMol Manual |Frequently Asked Questions |RasMol 2.7 Series History |RasMol and OpenRasMol |
| Click Here to Make a Donation |
Molecular Graphics Visualisation Tool
RasMol is a program for molecular graphics visualisation originallydeveloped by Roger Sayle. This site is provided for the convenienceof users and software developers of open source versions of RasMol.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.The 'Frequently Asked Questions' (FAQ) document for OpenRasMol is derived in part from two FAQs posted to the web by Eric Martz athttp://www.umass.edu/microbio/rasmol/faq.htm,one FAQ by Roger Sayle, and one by Eric Martz. The portions of theFAQs from the Martz web site are included by permission of Eric Martz.Many of the questions in thisdocument are the same or similar to those in the earlier FAQs, but someof the answers are different. If all or part of an answer is identical to given by Roger Sayle or Eric Martz, we will put that portion in quote marks and indicate the attribution by '--RS' or '--EM'.
Some of the responses to questions come from the RasMol manual.
The original RasMol manual was created by Roger Sayle. In July 1996,Dr. Margaret Wong of the Chemistry Department, Swinburne Universityof Technology, Australia, made extensive revisions to the RasMol 2.5manual to accurately reflect the operation of RasMol 2.6. Eric Martzof the University of Massachusetts made further revisions. In May1997, William McClure of Carnegie Mellon University reorganized theHTML version of the manual into multiple sections which could bedownloaded quickly and added use of frames. Portions of the 2.7.1version of the RasMol manual were derived with permission fromWilliam McClure's version using Roger Sayle's rasmol.doc for?version 2.6.4 as the primary source. Changes have been made inAugust 2000 for RasMol version 2.7.2.
The RasMol documentation was adapted for RasTop by PhilippeValadon in August 2000.
Edited by Philippe Valadon
Edited by Herbert J. Bernstein and Frances C. Bernstein
Contents
What is this document?
This document is a compilation of questions about RasMol that either have been asked with some frequency, or which the authors of this document think mightinterest people who use RasMol.
Why won't the RasWin.exe I just downloaded run?
Many web browsers try to download RasWin.exe and its help filesas if they were ordinary text files. They are all binary files.In some cases, a browser can be convinced to do a binary downloadby holding down one of the shift keys (Alt, Opt, Shift, etc.), whileclicking on the download link. If that does not work, then youwill have to download gzipped files and unpack them under Windows.Sometimes your browser will be willing to download the gzippedfiles as binary files, but if that does not work, you will have toresort to the File Tranfer Protocol (FTP) client packaged withall copies of Windows.
I get the message 'No suitable display detected!'
This is a problem on the UNIX version of RasMol caused by one oftwo potential problems. The first is that your DISPLAYenvironment variable isn't set corrrectly or that you don't havepermission to display to the X Windows server. This can bechecked by testing whether it is possible to run any other X Windows program.The second problem is caused by a mismatch between the configured version of RasMol and the display depths available on the current X Windows server. This is most often the case when RasMol has beencompiled in 24/32bit mode (by defining THIRTYTWOBIT in either rasmol.hor Makefile). The 24/32bit mode indicates that RasMol should use3bytes/pixel (or 16 million simultaneous colours). If the currentX Windows server is unable to display this visual depth it reportsthe 'No suitable display' error. The visual depths supported by the current X Windows server can be reported by typing the 'xdpyinfo' command. To solve the problem, recompile RasMol withEIGHTBIT defined instead (i.e use one byte/pixel or 256 simultaneouscolours).
Note: that RasMol must be configured with EIGHTBIT for 1bit/pixel(monochrome) or 8bit/pixel displays, with SIXTEENBIT for 16bit/pixeldisplays and with THIRTYTWOBIT for either 24bit/pixel or 32bit/pixeldisplays.
--RSIn pactice on most UNIX systems, the fastest way to change thepixel bit depth after a 'xmkmf' has been done, is to edit thefile 'Makefile', commenting out the wrong definition (i.e. ofEIGHTBIT, SIXTEENBIT or THIRTYTWOBIT) and uncommenting theright definition. Then 'make clean' followed by 'make' shouldcorrect the problem.
Why are there such long headers on these web pages?
We regret the necessity for the long headers. They are part of the hoops wehave to jump through to keep OpenRasMol programs and RasMol 2.7 series of releases in particular available as 'open source' software.(Please see the web page on Copyrights and Notices)
Can RasMol be distributed freely, on CD-ROMs, andused freely even for commercial purposes?
Different versions of RasMol have had different rules forredistribution. The rules for the RasMol 2.7 series are intendedto allow redistribution on an 'open source' basis.The idea is to encourage distribution of RasMol and programsderived from RasMol provided source code and documentationremain available, and a few other sensible conditions areaccepted by the distributor.
Starting with RasMol release 2.7.3, RasMol may be distributedunder the GPL, one of the most popularopen source licenses.
The specific rules for all recent RasMol releases are given in the file NOTICE.
Does this mean I can't make a commercial graphics programbased on RasMol?
If what you mean by 'commercial' is that you want to distributebinary versions and keep the source code as a secret, no, you may not do that, but if what you mean by 'commercial' is that you wishto sell programs and services based on RasMol, that you certainly may do.Just remember that your new and wonderful program has to include or referenceall the original source code and documentation, including the fileNOTICE, which will allow other people to copyyour program. In other words the rules for distributing copies ofRasMol that you have taken advantage of will also apply to people whowish to make copes of your program.
A lot of people find it easy to work within this framework, but if youneed to do commerical development which does not fit the open sourcemodel, you may not make use of any substantial portion of theRasMol 2.7 series to develop your own product.
What is the relationship between RasMol, Linux and the GPL?
RasMol 2.7 runs quite nicely under Linux. There are pre-compiled binariesof the 2.7 series to run under Linux. Starting with the RasMol 2.7.3release, RasMol may be distributed under the GPL.However, earlier RasMol 2.7 releases are not coveredby the GPL. Those RasMol 2.7 releases have their own 'GPL-like' license (RASLIC, which carefully avoidscertain issues which, until recently, would have caused problems if we had used the GPL for those releases. Those problems havenow been resolved, and we can now use the GPL.
Is RasMol 'Year 2000 (Y2K) compliant'?
RasMol 2.6 and all prior versions are fully Y2K compliant with a singlecaveat. RasMol can read and write MDL Mol and Brookhaven PDB files, whichreserve only two characters for the year in a date field. RasMol ignoresthese fields and is therefore not affected by Y2K. However programsreading MDL Mol files generated by RasMol (or any other molecular graphicsprogram) may suffer if they process the date field.--RS
In addition, please note that we are now well past 31 December 1999, andthere has not been a single report of a Y2K-related RasMol failure.
Is RasMol 'Euro compliant'?
IT managers in the 'euro-zone' need to assure themselves thatall software they use will support the Euro by January 1, 2002.RasMol does not deal with currency, and therefore is effectively'Euro compliant'. However, most existing versions of RasMol usethe Latin-1 (ANSI), Macintosh, or MS Windows OEM characters sets,without explicit support for the Euro symbol, which might causeRasMol to be rejected in testing for 'Euro compliance' against standardsintended for financial software. If this proves to be a nuisance,please contact EuroCompliance@OpenRasMol.org
What are the definitive literature citations for RasMol?
The currently preferred literature reference to RasMol is: Roger Sayle and E. James Milner-White. 'RasMol: Biomolecular graphics for all', Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.--RS
In addition the best reference for the 2.7 series is:Herbert J. Bernstein, 'Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455.
Where can I get more molecule co-ordinate files?
In addition to the example files that are distributed with RasMol the major source of data files for RasMol isthe Protein Data Bank operated by the Research Collaboratory forBioinformatics (see http://www.rcsb.org/pdb). This is the mainrepository for all of the world's known 3D xray-crystallography andnuclear magnetic resonance (NMR) structures of proteins and nucleicacids. Currently (September 2000) over 13,000 are available from mirrorsites throughout the world (see http://www.rcsb.org/pdb/mirrors.htmlThe primary archive for three dimensional structures of small moleculesis the Cambridge Crystallographic Data Centre, with over 200,000 organic andmetal organic compounds (see http://www.ccdc.cam.ac.uk). However,for many users, this resource is not available on-line.
A list of sites that hold small molecule co-ordinates (and additional proteinstructures) is Eric Martz'z 'Molecules Galore!' WWW page athttp://www.umass.edu/microbio/rasmol/whereget.htm
[This answer was derived in part from the RS response to this question. -- HJB]
Why won't RasMol 2.7 display my bond orders?
Older versions of RasMol infer bond orders from redundantCONECT records for some molecules in a psuedo-PDB format.Unfortunately, this would cause the display of incorrectbond orders for some valid PDB format files which hadredundant CONECT records for other reasons. The featurehas been disabled until a consistent and reliablealternative can be found.
How do I measure distances within RasMol?
There are two ways to measure distances between atoms in ..RasMol. The first is to use the 'set picking distance' command, to set the mouse into interactive distance measurement mode. Then by clicking on pairs of atoms, RasMol will report the distance between them on the command line. RasMol also has similar modes for 'set picking angles' and 'set pickingtorsions
'. The mouse can be returned to the default mode using 'set picking ident'.The second approach is to use distance monitors. A distance monitorin RasMol is a graphical dotted line between an arbitrary pair of atomsoptionally labelled by the distance between them. There are two waysto add a monitor to a molecule. The first is to use 'set pickingmonitors', similar to set picking distance above. Note that this willacta as a toggle and selecting the same two atoms again will remove themonitor. Monitors can also be added from the command line using themonitor command. This command takes the atom serial numbers of thetwo end-point atoms as parameters. All monitors can be turned of usingthe command 'monitors off'.
--RS
How do I select residues in a particular chain?
The method for selecting a range of residues in a particular chain .. improved in RasMol version 2.6. It can now be done using the syntax 'select 1-25:a' to select residues 1 to 25 in chain A. Similarly 'select 25:a' and 'select :a' will select just residue 25 in chain A and all of chain A, respectively.In RasMol versions prior to v2.6, you'd have to type an atom expression of the form 'select 1-25 and **a' where the final term is a primitive expression. This primitive expression is a wildcarded formof the form 'cys37a' where the residue name and number are replaced by the wildcard '*'.
Note that care has to be made to ensure that RasMol can determine which field is being specified. For example, although 'select *a' will select all residues in chain A, if the chain identifier was a number, 'select **1' would have to be used, as 'select *1' denotesresidue 1. To avoid any ambiguity, an optional colon character is now used to prefix the chain identifier, allowing expressions such as'cys:a', 'cys35:1', '*:1' and even just ':1'.
See also the RasMol Manual.
--RS
How can I create the PDB file for a particular sequence?
May I strongly recommend that you consider using the Swiss-Modelserver, written by Manuel Peitsch at the University of Geneva. Thise-mail and WWW server accepts as input either an amino-acid sequenceor a multiple sequence alignment with a protein of known structureand performs comparative homology modelling to return the potential3D structure to you by e-mail as a PDB file.For more information visit the Swiss-Model WWW page at www.expasy.ch/swissmod/SWISS-MODEL.html
--RSI can't find the command line window in RasWin
This is a confusing problem with RasWin. When RasWin startsunder Microsoft Windows the command line window is initially iconised(unlike the Macintosh or UNIX versions). The 'RasMol Command Line'icon appears at the bottom of the screen on the Windows background.Unfortunately, this is often obscured by another window such as theProgram Manager or the File Manager. Both the 'RasMol' icon and the'RasMol Command Line' icons can be seen if all the open windows are minimized.A more convenient solution is to make use of the Microsoft 'Alt-Tab'control key combination. Hold down the 'Alt'-key, and press the 'Tab' key one or more times until the name of the window you wish to bringto the front appears, then release the 'Alt'-key.
--RSHow do I create high resolution images in RasMol?
Unfortunately, raster images generated by RasMol are currently limited by the screen resolution (though this deficiency is actively being worked on).This means that images will generated at the resolution of about 72dpi(dots per inch) even though most printers (including colour printers) support resolutions of 300dpi, 450dpi or even 600dpi. This leads tojagged bitmap like printouts where the individual pixels are often visible.Regservo Download Windows 10
The exception to the above rule is images produced in Vector Postscriptformat using the 'write vectps' command. These output files have the advanatge of being generated at the printer's resolution, but the disadvantage of not supporting all of RasMol's representations.
One way to minimise the limitations of screen resolution is to expand ormaximise the RasMol graphics window to the full size of the screen before generating an output file. This ensures that the image contains as muchdetail as possible. Another commonly used trick is post-process the imagein a graphics package such as PhotoShop or 'xv' to expand and then bluror smooth the images generated by RasMol.
..
As mentioned above RasMol's resolution limitations are currently beingremoved by four approaches:
- Support for high resolution output images (at x4 screen resolution).
- The ability to have large resolutions in UNIX command-line only mode.
- Vector PostScript support for all RasMol representations.
- Export of model file formats (including POV, Raster3D, DXF and VRML) to other rendering programs such as photo-realistic ray-tracers.
Generating RasMol animations non-interactively in UNIX
The inability to use the save and write commandsin a RasMol script file is a deliberate security feature.There was a concern about the security of using RasMol on the Internet when researchers started e-mailing and FTPing 'untrusted' script files between sites. This was especially true of sites that have configured Netscape to fire up RasMol with a RasMol script file MIME type.Such a script, executed with 'rasmol -script <filename>' may potentially overwrite system and user files, for example creating a 'Rasmol Mac Os X Free Download
~/.rhosts' file on the remote machine. To defend against this threat I decided to disable the save and write command from within RasMol, unless the command 'set write true'had been entered interactively on the command line.The solution to the problem is to run your scripts with:ori.e. pipe the commands into stdin. RasMol can't tell that these haven'tbeen generated interactively and allows save and write commands.
--RSIs there an Acorn Archimedes version of RasMol?
The Acorn Archimedes (ARM) version of RasMol has been ported by MartinWuerthner at the University of Stuttgart,'wuerthne@trick.informatik.uni-stuttgart.de'. The Archimedes distribution is available at the following sites:HENSA (difficult to reach for users from outside the UK):micros.hensa.ac.uk (in /micros/arch/riscos/e/e089/rasmol.arc),the University of Kaiserlautern (Germany):ftp.uni-kl.de (in /pub/acorn/long/science/chemistry/rasmol.arc),and the University of Stuttgart (Germany):ftp.uni-stuttgart.de (in /pub/systems/acorn/riscos/etc/rasmol110.spk).
The first RISC OS release (1.10) of RasMol has the following features inaddition to those of the X version:
- runs on all Acorn 32-bit RISC computers under RISC OS 3.1 or higher, supports all display depths up to 24 bpp, just about runs on a 2MB machine
- fully supports RISC OS cooperative multitasking even while rendering the image
- Floyd-Steinberg colour dithering for 16 and 256 colour modes
- support of both the RasMol mouse mode and a more RISC OS-like way using a tool bar with rotation/translation/slabbing etc. tools
- extended menu structure (e.g. sub-menus to enter parameters for display options)
- exports native RISC OS bitmap format, RISC OS drag-and-drop support
--RS
The latest release for the Acorn is the RISC OS port of RasMol 2.7.1 (RISC OS port version 1.31b) (see http://www.mw-software.com/software/rasmol/rasmol.html).
Is there an MacOS X version of RasMol?
The short answer is yes -- see the sourceforge openrasmol site.
Why can't I see my data files in Classic under Mac OS X?
If you create data files under Mac OS X in order to load them intothe Classic version of RasMol, you may need to set the 'creator'and 'file type' of the files to make then visible to Classic.Apple provides a utility, SetFile, in the Developer Tools that will do the job.First you need to install the Developer Tools from CD or from the Appleweb site developer.apple.com/tools/download/. You should then be able to find SetFile at /Developer/Tools/SetFile. Usinga terminal window, change your directory to the one containing the file youcannot see and execute
/Developer/Tools/SetFile -t 'TEXT' filename
where filename is the name of the file you need to see as a PDBdata file in a Classic version of RasMol
--HJB
How do I see RasMol's stereo pairs in 3D?
See Gale Rhodes' excellent guide to viewing stereo image pairs,Stereo Viewing.--EM
Rasmol 2.7.5
What is the relationship among the various RasMol web sites?
There is no connection between the molecular graphics program RasMol andthe rasmol.com web site. The www.RasMol.org, www.OpenRasMol.org and www.OpenRasMol.com sites are all the same site, the home page for the molecular graphic program RasMol.Eric Martz's site www.umass.edu/microbio/rasmol/is focused on Protein Explorer and Chime. Even though it is badly outof date with respect to RasMol, it contains a great deal of usefulinformation, and maintains a discussion list for those interested inRasMol.
We have notified that holders of rasmol.com that they are causing confusion with our marks by using the name rasmol for their site, butthey have not, to date (15 June 2002), responded to our email. One might speculate that they are using the popularity of the name to draw 'eyeballs' for the advertising on their site. Please note thatthe RasMol project does not draw any revenue or other benefitfrom such advertising. -- HJB
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