[Chimera-users] Mesh points from volume data

[Michał Kadlof]

Works like a charm! :)

--
pozdrawiam serdecznie
Michał Kadlof <m.kadlof at cent.uw.edu.pl>

2016-09-06 19:28 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>
>
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> volumepathtracer/framevolpath.html>
>
> 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
> ----------
> 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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