Hello, I am using the icosahedron surface tool to build a triangulated sphere cage around a model. How can I write its coordinates? Thanks in advance, Yasser
Hi Yasser, You can change the vertices and edges in the icosahedron surface into a "molecule" (dummy atoms and bonds) with the "meshmol" command, and then save the resulting coordinates as a PDB file. For example, if your icosahedron surface is #0, command: meshmol #0 0.25 ...for bond stick-display radius 0.25; you could use some other number, doesn't really matter if the purpose is to save coordinates. That will create a new molecule model with name "Mesh Icosahedron." <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> ...and then use command "write" or menu: File... Save PDB to save that molecule model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2020, at 3:05 AM, Yasser Almeida <yasser.almeida@gmail.com> wrote:
Hello, I am using the icosahedron surface tool to build a triangulated sphere cage around a model. How can I write its coordinates? Thanks in advance, Yasser
Great, thanks! El mar., 30 jun. 2020 a las 17:09, Elaine Meng (<meng@cgl.ucsf.edu>) escribió:
Hi Yasser, You can change the vertices and edges in the icosahedron surface into a "molecule" (dummy atoms and bonds) with the "meshmol" command, and then save the resulting coordinates as a PDB file.
For example, if your icosahedron surface is #0, command:
meshmol #0 0.25
...for bond stick-display radius 0.25; you could use some other number, doesn't really matter if the purpose is to save coordinates. That will create a new molecule model with name "Mesh Icosahedron." <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>
...and then use command "write" or menu: File... Save PDB to save that molecule model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2020, at 3:05 AM, Yasser Almeida <yasser.almeida@gmail.com> wrote:
Hello, I am using the icosahedron surface tool to build a triangulated sphere cage around a model. How can I write its coordinates? Thanks in advance, Yasser
participants (2)
-
Elaine Meng -
Yasser Almeida