Re: [Chimera-users] Mesh points from volume data
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@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@cent.uw.edu.pl>
On Sep 6, 2016, at 12:36 PM, Michał Kadlof <m.kadlof@cent.uw.edu.pl> wrote:
Works like a charm! :)
-- pozdrawiam serdecznie Michał Kadlof <m.kadlof@cent.uw.edu.pl>
2016-09-06 19:28 GMT+02:00 Elaine Meng <meng@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@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@cent.uw.edu.pl>
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 …
On Sep 7, 2016, at 4:29 PM, Elaine Meng <meng@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@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@cent.uw.edu.pl>
On Sep 6, 2016, at 12:36 PM, Michał Kadlof <m.kadlof@cent.uw.edu.pl> wrote:
Works like a charm! :)
-- pozdrawiam serdecznie Michał Kadlof <m.kadlof@cent.uw.edu.pl>
2016-09-06 19:28 GMT+02:00 Elaine Meng <meng@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@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@cent.uw.edu.pl>
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Elaine Meng -
Tom Goddard