On Thu, Jul 17, 2014 at 11:33 PM, Eric Martz <[email protected]>
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
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