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