From: Andrew (
Date: Thu Dec 09 2010 - 18:47:43 CST


I would this feature useful as well. Would it work with "surf" too?


On Dec 9, 2010, at 2:40 PM, John Stone wrote:

> Hi,
> Old versions of MSMS supported this, and the "which atoms" mode
> chooser in VMD enabled one to compute the surface corresponding to
> all of the atoms, but trimmed it to show only the surface elements
> for the selected atoms (e.g. your "within" selection). This functionality
> was removed from the newer versions of MSMS, and doesn't work the the
> most recent MSMS binaries anymore. I could probably implement some code
> in VMD to post-process the mesh returned by MSMS to re-enable this kind
> of visualization. I haven't had anyone ask for it in years, until now.
> If people would find this functionality useful to have in VMD again,
> I could look into what it would take to implement it.
> Cheers,
> John Stone
> On Wed, Dec 08, 2010 at 01:15:02PM -0500, Joseph Bylund wrote:
>> I would like to generate a representation which shows the protein
>> surface within a cutoff distance of a feature of interest
>> (residue/ligand). When I change the selected atoms to "within 10 of
>> resid 100" or whatnot, it generates a surface based on the atoms inside
>> this selection rather than "cropping" the surface to this distance. Is
>> there a way to crop the surface rather than generate a different surface
>> based on the selection?
>> -Joe
> --
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