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

[Eric Martz]

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, also.

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 million?

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 
recently 
(http://www3.interscience.wiley.com/cgi-bin/abstract/113449000/ABSTRACT ).

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
http://bioinformatics.org/pipermail/molvis-list/2006q3/000345.html

I will be interested to read your report. Please send me a copy!

-Eric



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Eric Martz, Professor Emeritus, Dept Microbiology
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