Eric, you might try the PyMOL list for that as well. Lots of people there
that do specialized calculations like that.
Bob
On Fri, Jul 18, 2014 at 12:58 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> On Thu, Jul 17, 2014 at 11:33 PM, Eric Martz <ema...@microbio.umass.edu>
> wrote:
>
>> 1. Am I correct that "isosurface solvent volume" reports the volume
>> of the model? (I understand the distinction between solvent and
>> sasurface, and I prefer solvent.)
>>
>>
> yes
>
>
>
>> 2. If yes, in what units? Cubic Angstroms?
>>
>>
> yes
>
>
>> 3. With some large multi-chain protein assemblies, when I do
>> "isosurface solvent", the resulting surface has large holes in it.
>> What causes these, and do they cause the calculated volume to be
>> incorrect? (tsk tsk, I was using Jmol 14.0.13 -- I should redo those
>> with 14.2.2)
>>
>>
> No issue with versions in this case. Make sure that you add "only" to the
> isosurface command when you want a specific part of the model as a complete
> surface.
>
> isosurface select {*:C} *only* solvent volume
>
> Bob
>
>
>
>
>> Thanks, Eric
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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