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

A G Szabo agszabo at bell.net
Tue Nov 29 11:26:31 PST 2016


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

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: November-28-16 7:31 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] more questions about visualizing the backbone.

Hi Arthur,
Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”.  

Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector.  You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window.  In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true.

If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu:

Actions… atoms/bonds… hide
Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer)

You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections.

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 28, 2016, at 4:02 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> Last week I asked a question regarding about how to visualize the 
> backbone atoms. I have figured that out.
> 
> I am working with a peptide that forms an amyloid structure.  The 
> peptide strands form a beta sheet. When I select two of the peptide 
> units that are hydrogen bonded to form two strands in the beta sheet, 
> the strands are shown as a coil type structure rather than a flat beta strand.
> 
> How can I change the coil backbone to a beta strand structure?
> Second part is there a simple way to suppress the side chains but 
> leaving the backbone atoms?
> 
> I have included two peptide units that are hydrogen bonded to one another. 
> Thanks
> 
> Arthur G. Szabo





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