[Chimera-users] Mesh points from volume data

[Tom Goddard]

It is easy to access the Chimera density map surface vertices and triangles in Python.  I’ve attached a bit of Python code triangles.py that illustrates this, just open a map, then open this script in Chimera.  Below is example output.  More Python Chimera script examples are on the Chimera developer wiki.

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

  Tom

emd_1080.map map, 21656 vertices, 43200 triangles
vertex coordinates:
   -22.218    -43.2    -64.8
   -20.904    -43.2    -64.8
     -21.6  -43.508    -64.8
     -21.6  -42.459    -64.8
     -21.6    -43.2  -64.871
...
triangle vertex indices:
       0      4      2
       3      4      0
       1      2      4
       3      1      4
       5      9      7
…

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> On Sep 7, 2016, at 4:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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