[Chimera-users] question

A G Szabo agszabo at bell.net
Fri Dec 2 09:33:56 PST 2016

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 model.

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 <frameatom_spec.html> 

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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