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>