[Chimera-users] simple question

A G Szabo agszabo at bell.net
Fri Nov 25 11:52:40 PST 2016


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


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: November-25-16 11:24 AM
To: A G Szabo
Cc: chimera-users at 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 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 at 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

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