[Chimera-users] Script to generate and fit structures

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 12 14:19:35 PDT 2019

Hi Ahmad,
In that case, if you know the repeating symmetry of the structure, you could add copies of the atomic structure with command “sym” (figuring out or describing the symmetry correctly can be difficult, however).  For fitting into maps, see command “fitmap.”



> On Jun 12, 2019, at 10:08 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> I meant fit into density, it's a microtubule map with lots of tubulin monomers. I'm trying to build the entire structure into density from a single monomer in an automated way. 
> On Wed, Jun 12, 2019, 12:44 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> A command script is just a text file that has the same commands you would type in the command line.  So, you just have to figure out by trial and error (typing them into the command line individually) which commands you want to put in the file.
> See commands: combine, move, savepos, reset, maybe also tile
> I don’t know what you mean by “fit it into its new place,” but if you mean superimposing one structure on another, see commands matchmaker and match.
> List of all commands, click links to see details on each one:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> General explanation of command files and links to examples:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

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