[Molvis-list] Use statistics on macro-molecular visualization programs

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Sun May 27 21:35:28 EDT 2007

For those who may be interested, downloads of RasMol from the primary
rasmol.org site continue at a steady rate of more than 100K per year.
The week before last we had over 2200 downloads, including:

   1400 MS Windows
    500 Linux
    296 Mac

There are also small numbers of downloads for HPUX, Dunix and IRIX binaries.

This would put us on track for well over 100K downloads a year, as usual.
The windows installer is the most popular single download, accounting
for almost half the windows binary downloads.

These stats are just for that one site, not for other sites or means
of distribution, such as CDs.

At 12:52 PM +0900 5/27/07, Eric Martz wrote:
>At 5/25/2007, Liz Huysamen wrote:
>>Dear Mr Martz
>>I'm writing to you as a biochemistry post-grad student, doing a
>>thesis-project on students and molecular modeling. I've searched
>>repeatedly, but cannot locate any statistical information regarding
>>usage of the most popular 3D display programmes (Protein Explorer,
>>RasMol, etc.). Would you be able to help me locate this information?
>>Kindest regards,
>>Liz Huysamen (BSc; UKZN, South Africa).
>Dear Ms. Huysamen,
>I am not aware of any single organized source of usage information. 
>I'll try to help, as these data are of considerable interest to me, 
>It will be useful if you distinguish "modeling" from 
>"visualization". Under separate cover, I'll send some definitions. 
>RasMol, Jmol, Chime and Protein Explorer do no modeling. DeepView 
>does serious modeling; PyMol does a little.
>It is probably impossible accurately to gage general use of 
>stand-alone applications such as RasMol. However, one can look at 
>downloading rates. Of course, many downloads may never be used much, 
>many may receive a copy from a friend and use it without 
>downloading. I have not bothered to obtain the download stats for 
>Rasmol from my umass.edu site in recent years. In the third table, 
>last column here ( http://www.umass.edu/microbio/chime/vistats.htm ) 
>you will see that from 1997-2003 RasMol 2.6 was downloaded from this 
>one site 50,000 - 100,000 times/year. Plus there are many other 
>sources for it. In particular, I think if you contact Herb Bernstein 
>(yaya at bernstein-plus-sons.com) he may be able to provide stats for 
>RasMol 2.7 from http://rasmol.org which he manages. (He received 
>this already via molvis-list; see below.) I suspect there are 
>hundreds of thousands of RasMol users worldwide, perhaps close to a 
>I urge you to ask your questions on at least four email lists:. 
>molvis-list, pdb-l, jmol-users, and the deepview list. All are 
>linked to http://molvisindex.org under email discussions. I have 
>taken the liberty of copying this email to molvis-list and jmol-list 
>in the hopes that it will evoke some additional information.
>From jmol-users, someone will hopefully provide you with download 
>rated for jmol. Jmol is superceding Chime because it is more 
>powerful, cross-platform, open-source and very actively developed, 
>and can be used both as a stand-alone application and an applet in 
>browser-based tutorials and applications (such as FirstGlance in 
>Jmol, FJmol, http://firstglance.jmol.org). If you go to 
>http://proteinexplorer.org you'll see a comparison of PE with FJmol. 
>Jmol was published in Biochemistry and Molecular Biology Education 
>You could try contacting MDL Information Systems, specifically Tom 
>Blackadar (Tab at mdli.com, to whom I've copied this) for Chime 
>download stats. I suspect someone there has kept historical records, 
>which would be of considerable interest to many (1996-present).
>The first widely used, free software capable of macromolecular 
>visualization was David Richardson's MAGE and his and Jane 
>Richardson's Kinemages, starting in 1992. RasMol was first offered 
>in 1993, and Chime in 1996. Jmol did not become 
>macromolecule-capable until about 2004, although the Jmol project is 
>much older. Some historical info is at the history site I 
>co-authored with Eric Francoeur ( 
>http://www.umass.edu/microbio/rasmol/history ). Recently, Richardson 
>provided KiNG (Kinemage New Generation), a java applet. Perhaps he 
>can provide some usage stats? (I've copied this to him.)
>It is useful to distinguish structural biologists 
>(crystallographers, NMR spectroscopists, and professional modelers) 
>from non-structural biologist users of visualization software. See 
>the last paragraph in the editorial in Nature Structural and 
>Molecular Biology 14:1, "Looking ahead with structural genomics" 
>(January 2007; http://www.nature.com/nsmb ) -- I can send you the 
>PDF if you have trouble getting it. (For a definition of structural 
>genomics, see http://bioinformatics.proteinexplorer.org/stgenomx.htm 
>PyMol has increased in popularity dramatically in recent years among 
>crystallographers. I saw one recent estimate that 30% of 
>crystallographic figures in journals are now make with PyMol (but I 
>don't recall where I saw that ...). Though it is quite powerful, and 
>its images are at the top in "beauty", PyMol is not user-friendly, 
>and not much used by non-structural biologists. The latter are more 
>likely to use RasMol, Chime, Protein Explorer, Jmol, or FirstGlance 
>in Jmol.
>For on-line applications such as Protein Explorer (PE) and 
>FirstGlance in Jmol, automatic visitor counting meters can gather 
>use information. I have kept up to date stats for many of my sites. 
>This spring, there were 2,371 visitors to Protein Explorer's 
>FrontDoor per week (page views/week is about 2.5 fold higher than 
>visitors/week). I have a meter in Protein Explorer's QuickViews. To 
>get there, you have to have a compatible browser with Chime 
>installed, and then go beyond the first two control panels 
>(FirstView and Features of the Molecule) to QuickViews. 400 
>visitors/week online, plus >100/week using downloaded PE, accessed 
>QuickViews. The number of visitors to the FrontDoor was the same in 
>spring 2006; the QuickViews uses/week were 100 higher (total 
>600/week). In 2005, again FrontDoor visits were the same, and 
>Quickviews uses/week 100 higher again (total 700/week). So 
>QuickViews use has fallen a couple of hundred/week. Perhaps those 
>sessions are now on FirstGlance in Jmol, which averaged 644 
>sessions/week this spring. ("Spring" here means the high volume 
>season, from February 1 through mid-May.)
>Another way to judge use is by citations in scientific journal 
>articles. In Sept 2006, I gathered some of these stats from 
>highwire.stanford.edu -- see
>I will be interested to read your report. Please send me a copy!
>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Eric Martz, Professor Emeritus, Dept Microbiology
>U Mass, Amherst -- http://www.umass.edu/molvis/martz
>Biochem 3D Education Resources http://MolviZ.org
>See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
>Protein Explorer - 3D Visualization: http://proteinexplorer.org
>Workshops: http://workshops.proteinexplorer.org
>World Index of Molecular Visualization Resources: http://molvisindex.org
>ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
>Atlas of Macromolecules: http://atlas.proteinexplorer.org
>PDB Lite Macromolecule Finder: http://pdblite.org
>Molecular Visualization EMail List (molvis-list):
>       http://bioinformatics.org/mailman/listinfo/molvis-list
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  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  yaya at dowling.edu

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