[Chimera-users] more questions about visualizing the backbone.

A G Szabo agszabo at bell.net
Wed Nov 30 15:06:35 PST 2016


Elaine

Thank you very much that is very helpful.

arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: November-30-16 12:37 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] more questions about visualizing the backbone.

Hi Arthur,
I guess our Actions menu menu “backbone” isn’t including the hydrogens.

You could display backbone hydrogen atoms by their names using the command line.   If you have proteins that use the standard atom names, then this should work:

disp protein & @h,ha,h1,h2,h3,ha1,ha2,ha3

…or if you only want the ones on backbone nitrogens (not on the alpha-carbons):

disp protein & @h,h1,h2,h3

For your other question, you are selecting or “picking” with the mouse on the structure, Ctrl-click selects one atom or bond and you can add to that selection with Shift-Ctrl-click, as desribed in:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Pardon the delay, I was away from work yesterday.

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 29, 2016, at 11:26 AM, A G Szabo <agszabo at bell.net> wrote:
> 
> Elaine
> Sorry for asking so many what are likely trivial questions.
> 
> When I visualize one chain from the whole model, I have figured out how  to produce a nice ribbon backbone I can visualize all the atoms of the peptapeptide. I can hide the side chains leaving just the backbone atoms along with the ribbon I have generated.  When all the atoms are visualized including the  side chains and the backbone atoms, all the hydrogen atoms in the peptide, including the ones on the  backbone nitrogen are shown. However, if I hide that  side chains and visualize all atoms of the backbone, all the hydrogens  on the backbone atoms disappear.
> 
> Because I am trying to show the hydrogen bonding between adjacent chains in the extended beta  sheet I would like  to keep those hydrogens, but not the side chains. The latter just clutter the image.
> 
> Comments?
> Thanks
> arthur




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