[Chimera-users] Mesh defined by distance to selection

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 21 13:04:24 PST 2015

Hi Mike,
Volume Viewer zoning does not create the mesh.  Instead it acts on a pre-existing density map shown with mesh isosurface; it hides the isosurface parts beyond the zone.

You can “fake” a density map for a set of atoms using the “molmap” command.  Basically this uses the positions of the specified atoms and smears them out.  Then in Volume Viewer, you could show the density map with a mesh isosurface, then select some of the original atoms and show only the mesh in the zone of those atoms.

However, you may need to experiment with the resolution and which atoms should be specified in the molmap command, the isosurface contour level, etc. and I don’t know how well the result would match what you have in mind.

Some example molmap commands:
molmap protein 6
molmap :1-100.A at CA 5

… see the man page for an explanation of how it works and additional command-line options:

Volume Viewer docs:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 21, 2015, at 10:45 AM, R. Michael Sivley <mike.sivley at vanderbilt.edu> wrote:

> I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for.
> I found this in the Chimera help pages, and it seems to be exactly what I need:
> http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#zone
> I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful.
> Could you help me identify the missing step in this process? Thanks!
> Mike Sivley
> PhD Student in Biomedical Informatics
> Center for Human Genetics Research
> Vanderbilt University

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