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

Yogendra Ramtirtha ramtirtha.yogendra at gmail.com
Mon Dec 21 23:32:21 PST 2015

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


On Tue, Dec 22, 2015 at 12:27 AM, Elaine Meng <meng at 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 at 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
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