From: John Stone (
Date: Thu Dec 09 2010 - 16:40:35 CST

  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.

  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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