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

On Tue, Dec 22, 2015 at 12:27 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Yogendra,
The website is fine, as far as I can tell. There is a PDF version of the whole User’s Guide linked to the documentation index, but it is very large (hundreds of pages):
<http://www.rbvi.ucsf.edu/chimera/docindex.html>

However, there is also a 2-page PDF Quick Reference Guide, mostly about commands, linked to the tutorials index:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf>

The Quick Ref lists mosts commands, and if you need details on a specific command, you could use the “help” command to see its HTML manpage (for example, command: help color).
Best,
Elaine
----------
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 2:45 AM, Yogendra Ramtirtha <ramtirtha.yogendra@gmail.com> wrote:
>
> I would be prefer me a PDF version of the user's guide to run commands through the command line
> Is the Chimera home page down ?
>
> Thank you,
> Yogendra