VMD-L Mailing List

From: Andrew (afenley_at_vt.edu)
Date: Thu Dec 09 2010 - 18:47:43 CST

Hi,

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

Cheers,
Andrew

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
> vmd_at_ks.uiuc.edu
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078