[Chimera-users] Mesh points from volume data

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 6 10:28:24 PDT 2016

Hi Michal,
You can use the “meshmol” command to make the isosurface mesh into a fake molecule, where the the points are “atoms” and the mesh lines are “bonds” shown as sticks. 

Although the new “molecule model” is suppressed from appearing in the File… Save PDB dialog, you can still save it to PDB from the command line with “write” … or save it as a marker set using the File menu of the Volume Tracer tool.

Either of those formats will contain the coordinates.  The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you.
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 Sep 6, 2016, at 6:48 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> Hello,
> I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation.
> How can I do that?
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl>

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