[Chimera-users] Mesh points from volume data

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 7 16:29:50 PDT 2016


Hello,
Sorry, I can’t help on this one, so I’m forwarding to the list!
Best,
Elaine

On Sep 7, 2016, at 6:24 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:

> Hello,
> 
> I'm almost home. There are several issues:
> 1. I need not only points but also planes -> point triples from surface triangulation.
> 2. I have quite a lot of points (more than 30 000). PDB file format fails in the CONNECT records:
> 
> In the end of file they looks like this:
> CONECT3051230171301923050530506
> CONECT3051230511
> CONECT3051330165301663018830508
> CONECT3051330514
> CONECT3051430188302133050830509
> CONECT305143051330515
> CONECT3051530213302163050930510
> CONECT305153051430516
> CONECT3051630193302163021830510
> CONECT305163051130515
> END
> 
> Is there any walkaround? Preferably it would be best solution for me if I could access both points and planes (faces) programatically with python. Is it possible?
> 
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl>
> 
> > On Sep 6, 2016, at 12:36 PM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> >
> > 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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