For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog. Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh. For molecular surfaces computed from atoms, change the vertex density as described here http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html> Tom
On Jul 31, 2018, at 5:53 AM, עמיחי הולצר wrote:
And another question - there is "Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh not to be so dense. Is it possible?
Thanks again!
2018-07-31 13:38 GMT+03:00 עמיחי הולצר : When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh?
Thanks, Amichai
2018-07-30 19:37 GMT+03:00 Tom Goddard : Hi Amichai,
Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>
Tom
On Jul 29, 2018, at 3:06 AM, עמיחי הולצרwrote:
Hi Chimera support,
I have 2 questions:
1. How does Chimera calculate the mesh from the density map?
2. How can I save the mesh as a file?
Thanks a lot, Amichai Holzer Huji _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>