Elaine Thanks for trying to help. I looked at the command ribbackbone atom-spec but because I rarely use the command line I am not very familiar with what some of the designations mean. I have a C-terminal Alanine, residue 42, in the chain C #0.8. Using the menu method I was able to visualize the C-terminal carboxyl and the Ala side chains. But as you indicated this seems to float from the backbone. The bond between the N in Ala backbone is not connected to residue 41, there is a small space. So my main question is what are the parameters that I should use with the command "ribbackbone"? Thank you Arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-25-16 11:24 AM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] simple question Hi Arthur, If you are showing ribbon, it suppresses the display of backbone atoms. To enable showing both backbone atoms and ribbon at the same time for the same residue, you would need to use command "ribbackbone". (Then you may still need to display the atoms after that.) Alternatively you can hide the ribbon for just that residue (e.g. select it and then use Actions.Ribbon. hide) and then show whatever of its atoms that you want. However, it will then be detached from the rest of the ribbon and look like it is floating. Yet another approach is to not use any ribbons for that figure. I hope this helps, 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 Nov 24, 2016, at 4:21 PM, A G Szabo <agszabo@bell.net> wrote:
I should be able to find this but haven't looked too hard.
I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue.
How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked.
Thanks
AGSzabo