[Molvis-list] RE: Molvis-list Digest, Vol 31, Issue 7

Warren DeLano warren at delsci.com
Mon May 28 14:43:23 EDT 2007


Liz & List,

For what it's worth, these days PyMOL is doing about the same download
volume as RasMol:  

PyMOL Downloads, April 2007		
		
Windows       8155     75%
Mac           1679     15%
Linux         1081     10%
Total        10915    100%

That's about 130k/yr but downloads are up a bit lately, so in fact, we
have logged only 235k downloads over the trailing 24 months.

In terms of older FREE builds (for everyone) versus CURRENT incentive
builds (for sponsors only), the vast preponderance of PyMOL downloads
(~90%) are for the older FREE versions, which lag the current code by
around two years in terms of features, compatibility, and bug fixes.
Regardless, Open-Source PyMOL source-code remains both FREE and CURRENT,
and DeLano Scientific LLC also gives full-time students and their
teachers FREE access to CURRENT precompiled builds upon request
(http://pymol.org/educational.html).  

As for popularity, over 60% of posters and talks at the recent West
Coast Protein Crystallography Workshop used PyMOL for at least one
figure (or movie).  However, that compares to only about 25% of
computational chemistry posters at the most recent Chicago ACS meeting,
and that is also about what you get when you scan mainstream journals
for structural biology figures over the past few years.  These numbers
are informal and not rigorously confirmed, but my best guess is that
PyMOL currently has at least a quarter of the overall macromolecular
visualization market (free or otherwise).  However, Erik is quite
correct that PyMOL does not have many users doing small-molecule,
quantum, materials-science, or multiscale visualization.

The good news is that PyMOL is self-sustaining at this level without
relying upon government grants, venture-capital funding, pure
volunteerism, or internal corporate subsidy (profits from other
products).  In fact, economically speaking, as far as I know, it is the
only independently-viable open-source molecular visualizer.  Thus, so as
long as people continue to use and sponsor PyMOL at present levels, it
should be actively developed and maintained under present terms as both
an open-source and commercially-maintained product -- hopefully the best
reasonable compromise between multiple worlds:  open-source, academic,
and commercial.  

With respect to academic use, the source code is unrestricted BSD
open-source.  This means that developers, scientists, and teachers can
create and redistribute their own derivative works that rely upon or
encapsulate PyMOL source code, without being encumbered by draconian
GPL-like conditions, provided that the appropriate PyMOL copyright
notices are preserved.

Yes, PyMOL is still too complex and confusing for some, but there have
been a number of usability improvements made over past years, and they
are helping more and more people ease up that steep PyMOL learning
curve.  Indeed, big pharma is at last starting to take PyMOL seriously
as a communications tool for medicinal chemistry and beyond.

Finally, there is a global community based around the PyMOL mailing
list, the Wiki, and dozens of end-user web sites.  Honestly, these folks
do a far better job supporting and enabling PyMOL use than does DeLano
Scientific (at least so far...that may eventually change).

Cheers,
Warren

Main page at: http://www.pymol.org

--
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice: 1-650-283-6945   Fax: 1-650-989-4082
US Mail: PO Box 1118, Palo Alto, CA 94302-1118, USA


> -----Original Message-----
> From: 
> molvis-list-bounces+warren=delsci.com at bioinformatics.org 
> [mailto:molvis-list-bounces+warren=delsci.com at bioinformatics.o
rg] On Behalf Of molvis-list-request at bioinformatics.org
> Sent: Monday, May 28, 2007 9:13 AM
> To: molvis-list at bioinformatics.org
> Subject: Molvis-list Digest, Vol 31, Issue 7
> 
> Send Molvis-list mailing list submissions to
> 	molvis-list at bioinformatics.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
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> 
> Today's Topics:
> 
>    1. Re: Use statistics on macro-molecular visualization	programs
>       (Herbert J. Bernstein)
>    2. Re: Use statistics on macro-molecular visualization	programs
>       (Herbert J. Bernstein)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 27 May 2007 21:35:28 -0400
> From: "Herbert J. Bernstein" <yaya at bernstein-plus-sons.com>
> Subject: Re: [Molvis-list] Use statistics on macro-molecular
> 	visualization	programs
> To: "Molecular Visualization,	especially in education with freeware"
> 	<molvis-list at bioinformatics.org>,	"Lizanne Huysamen"
> 	<203506034 at ukzn.ac.za>
> Cc: Tab at mdli.com, dcr at kinemage.biochem.duke.edu,
> 	molvis-list at bioinformatics.org
> Message-ID: <a06230901c27fd7fad0b9@[192.168.2.100]>
> Content-Type: text/plain; charset="us-ascii" ; format="flowed"
> 
> 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, 
> >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/11344900
0/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
> >
> >
> >
> >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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
> >- - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >
> >_______________________________________________
> >Molvis-list mailing list
> >Molvis-list at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/molvis-list
> 
> 
> --
> =====================================================
>   Herbert J. Bernstein, Professor of Computer Science
>     Dowling College, Kramer Science Center, KSC 121
>          Idle Hour Blvd, Oakdale, NY, 11769
> 
>                   +1-631-244-3035
>                   yaya at dowling.edu
> =====================================================
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 27 May 2007 21:35:28 -0400
> From: "Herbert J. Bernstein" <yaya at bernstein-plus-sons.com>
> Subject: Re: [Molvis-list] Use statistics on macro-molecular
> 	visualization	programs
> To: "Molecular Visualization,	especially in education with freeware"
> 	<molvis-list at bioinformatics.org>,	"Lizanne Huysamen"
> 	<203506034 at ukzn.ac.za>
> Cc: Tab at mdli.com, dcr at kinemage.biochem.duke.edu,
> 	molvis-list at bioinformatics.org
> Message-ID: <a06230901c27fd7fad0b9@[192.168.2.100]>
> Content-Type: text/plain; charset="us-ascii" ; format="flowed"
> 
> 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, 
> >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/11344900
0/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
> >
> >
> >
> >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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
> >- - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >
> >_______________________________________________
> >Molvis-list mailing list
> >Molvis-list at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/molvis-list
> 
> 
> --
> =====================================================
>   Herbert J. Bernstein, Professor of Computer Science
>     Dowling College, Kramer Science Center, KSC 121
>          Idle Hour Blvd, Oakdale, NY, 11769
> 
>                   +1-631-244-3035
>                   yaya at dowling.edu
> =====================================================
> 
> 
> ------------------------------
> 
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list
> 
> 
> End of Molvis-list Digest, Vol 31, Issue 7
> ******************************************
> 
> 
> 
> 


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