[Chimera-users] question

A G Szabo agszabo at bell.net
Fri Dec 2 11:21:41 PST 2016


The essential issue is that all of the Atoms of Gly are part of the
backbone. So in order to visualize those atoms one has to turn them on with
ribbackbone. But visualizing the backbone atoms of other residues with
longer side chains clutters up the image, and I would rather have the
backbone atoms of such amino acids turned off.

I sent you a power point attachment with the structure I am working with.
This is the partial structure of a beta sheet amyloid made up of the same
peptide all in a stack. So in order to show the key intramolecular
interactions in one of the peptides in the stack one can show the selected
residues. Only issue is that one cannot visualize Gly in any meaningful way
unless ribbackbone is turned on.

Thanks for your assistance

Much appreciated


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: December-02-16 12:47 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] question

Hi Arthur,
Unfortunately "ribbackbone" only applies to the whole model.  However, it is
merely an "enabler" allowing backbone atoms and ribbon to be shown at the
same time, if the atoms and ribbon both happen to be displayed for the same
residue.  You can still hide (~display) any atoms you don't want to see and
hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to

So you would have to use "ribbackbone #0.1" or something like that on the
whole model, but then hide all the atoms you don't want, say "~disp #0.1" to
hide all atoms, and then to show all atoms of glycines 33,37,38 it could be
something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain
A of model #0.1).

Again, you can use Selection Inspector instead of commands for many things,
although commands are better for doing things with specific residue numbers.
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 Dec 2, 2016, at 9:33 AM, A G Szabo <agszabo at bell.net> wrote:

> You have been very helpful in explaining different  items that use the
command line.
> I have a PDB file that was determined by NMR. Thus there are a large
number of chains number as pdb (#0.1) Chain A   etc.
> So I know that I can select a single chain, and build up an image with
Chains A, B, etc using the #0.1 chain number.
> I want to visualize three Gly residues in one chain. So I learned that I
can use the command ribbackbone  to visualize the backbone atoms of the
amino acids that I  want to show. So when I use that command all the
backbone atoms of the residues selected are visualized including the side
chains. I also know that if I use the command ~ribbackbone  all the backbone
atoms are suppressed leaving only the atoms of the side chains. I  know that
without any residues or atoms specified the command applies to the whole
> Now as I said that I  want to visualize three Gly residues in one of the
chains. The Gly residue numbers are 33, 37, 38.  They are on Chain #0.1 K.
> The information on the ribbackbone  in the  Chimera users guide, 
> indicates that I should be able  to do this by using parameters termed 
> atom-spec.  i.e. ribbackbone  atom-spec
> I looked elsewhere for how to designate the parameters for atom-spec and
tried a few things, but I was not able to achieve the specificity of showing
the backbone atoms of only the Gly residues. I don't think that I have to
indicate that I want only the Gly residues in Chain K #0.1 because I can
select the Gly residues from the sequence of Chain K #0.1.
> So after this long description of what I want to do, would you kindly
inform me of how I can visualize the backbone atoms of only Gly.
> Thank  you
> Arthur G. Szabo

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