[Chimera-users] Chimera User's guide for command ine usage

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 22 10:00:22 PST 2015

Dear Yogendra,
Sorry, no.  Chimera does not translate the things you do in the menu and tool GUIs into a list of commands.

In many cases if you look at the Help for the part of the menu or GUI tool that you are using, it will mention what commands are similar and link to their manual pages, but you would still have to figure out the exact commands yourself.  Also, the Getting Started tutorials include “menu” and “command” parts that cover mostly the same things as each other.


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 21, 2015, at 11:32 PM, Yogendra Ramtirtha <ramtirtha.yogendra at gmail.com> wrote:

> Can chimera give me a report of all the command equivalents of the different manipulations I manually do in the GUI.
> ex - if I open a PDB file, select a particular chain, delete ligands in that chain and save the same chain in Mol2 format. Can chimera give me a ".cmd" file of all the commands such that if I run the ".cmd" file in the terminal (in Ubuntu ) without using the GUI, I can reproduce the same results ?
> Can you guide me regarding this ?
> Thank you
> Regards,
> Yogendra

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