[Molvis-list] CORRECTED Molecular viewers in the literature

Eric Martz emartz at microbio.umass.edu
Sat Sep 30 20:40:17 EDT 2006

At 9/30/06, Egon Willighagen wrote:
>On Saturday 30 September 2006 03:40, Eric Martz wrote:
> > Numbers of hits searching full text of scientific journals at
> > highwire.stanford.edu:
> >
> > 2,364 Jmol
>Pardon?? Theses are Jmol word counts, correct? Any idea on the number of
>article this corresponds to?

>It really supprises me we outrank these... any clue? I thought PyMol was used
>a lot to create figures in bio articles...

The above was the jmol-users list. Also, on molvis-list, Wayne Decatur and 
Philippe Valadon kindly gave evidence that I included a huge number of 
false hits for "jmol".

OK, I have to retract the hastily gathered count above. It is for number of 
articles with searchable full text via highwire.stanford.edu, BUT the vast 
majority of the hits are not for the Jmol molecular visualization 
application/applet. Turns out "jmol" is a commonly used term with many 
meanings in science papers. The key fact is that 1,836 of the above hits 
are in articles published before 1995!

Since January, 2000 "jmol" occurs in 107 articles.
But over half of these seem to be "other" jmol's.

The best search I came up with is

(jmol and (chime or pymol or rasmol)) or jmol.org or jmol.sourceforge

which gave 54 hits, 52 of which are since 1995.

(jmol and 3d) did not work since 2/3 of the hits were before 2000.

The result of ~50 papers could be an underestimate, but by less than 
two-fold if we assume there are few if any valid jmol hits before the year 

So, here is the revised list:

1,406 PyMol (1,400 since year 2000)
1,132 RasMol (all since 1991; rasmol was first released in 1992)
   514 kinemage or kinemages (all since it was released in 1991)
   106 "protein explorer" not "membrane protein explorer" (since 1998)
   ~50 (jmol and (chime or pymol or rasmol)) or jmol.org or jmol.sourceforge
    33 webmol
    25 rastop
     5 QuickPDB
     1 FirstGlance in Jmol

Not easily disambiguated from false hits:
  - VMD
  - jmol (but see above)
  - Protein Workshop
  - KiNG

I apologize for my error. -Eric

Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US

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