[Chimera-users] question

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 2 09:46:39 PST 2016


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 see.

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
-----
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 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
> 
> 
> 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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