>Date: Sun, 27 May 2007 12:52:22 +0900 >To: "Lizanne Huysamen" <[EMAIL PROTECTED]> >From: Eric Martz <[EMAIL PROTECTED]> >Subject: Use statistics on macro-molecular visualization programs >Cc: [EMAIL PROTECTED], [EMAIL PROTECTED], >[EMAIL PROTECTED] > >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 >([EMAIL PROTECTED]) 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 ([EMAIL PROTECTED], 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 > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >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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