Vincent,
OK, Jmol 11.9.7_dev at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip should have a
PQR reader that reads this information correctly and will display the
cavities as desired. Note that since there is essentially no distinguishing
feature between PDB and PQR files, you must add the prefix
PQR::
to the filename in the LOAD command in order to bypass Jmol's file typing
algorithm. The following works for me:
load "PQR::pocket.pqr"
isosurface sasurface 0
It might be interesting to compare the results you get from this with Jmol's
own isosurface CAVITY feature. (See the documentation on that for details.)
It uses a slightly different idea, I think - spheres positioned on a regular
grid are "inflated" until they touch the protein at a given probe radius. In
either case you could measure the cavity's volume and area to see what sort
of differences arise.
Bob
On Tue, Oct 20, 2009 at 11:10 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> I just sent Vincent a message but will reiterate here:
>
> Jmol reads those DX files just fine. You must read them using the
> ISOSURFACE command:
>
> isosurface "xxxx.dx"
>
> Jmol is misreading that "PQR" file because people have "adapted" that
> format and this file does not strictly conform to the original definition
> (which was column-based). I'll have a fix for that today or tomorrow.
>
> Bob
>
>
>
> On Tue, Oct 20, 2009 at 2:04 AM, Vincent Le Guilloux <
> vincent.le-guill...@univ-orleans.fr> wrote:
>
>>
>>
>> Angel,
>>
>> As robert said, I don't thing open DX is the format I use. Even if the
>> link provided in the software point to a software seems related of
>> IBM's Data explorer. I've tryed to load my own example but jmol failed.
>>
>> Robert,
>>
>> Apparently, the radius colmumn is either not read, or not interpreted.
>> I've tryed all of your commands, and the result is always the same:
>> all my PQR probes have the same (displayed) radius, whatever surface
>> or spacefill method set. Note that JMolm seems to consider my probes
>> as phosphorus.
>>
>> I'm gonna send you two files corresponding to both cases.
>>
>> In any case, thanks you both for your answers.
>>
>> Vincent
>>
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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