Chimera User's guide for command ine usage
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
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
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
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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> 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 11:32 PM, Yogendra Ramtirtha <ramtirtha.yogendra@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
participants (2)
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Elaine Meng -
Yogendra Ramtirtha