I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place. Is it feasible, how can I do it? Regards.
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
On Jun 12, 2019, at 5:15 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place.
Is it feasible, how can I do it?
Regards.
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@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
On Jun 12, 2019, at 5:15 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place.
Is it feasible, how can I do it?
Regards.
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.” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> Best, Elaine
On Jun 12, 2019, at 10:08 AM, Ahmad Khalifa <underoath006@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@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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