[Chimera-users] showing backbone for some residues and not others

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 2 12:38:13 PST 2016


Hi Arthur,
I believe I understand completely, but I can only repeat my suggestions from before.  You would use “ribbackbone” to allow both ribbon and backbone atoms, and then use “disp” to show the atoms you want to see and “~disp” to hide the atoms you don’t want to see.  Don’t know what you mean by “didn’t work”.

The exact disp and ~disp commands depend on the models, chains, residues,…. in your structure.

Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30;  everything in that structure is chain A:

open 2gbp
ribbackbone
~disp
disp #0:40-50.A
disp #0:20-30.A & with CA/C1’

The last part of the last line means sidechains only.  However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before:

disp #0:20-30.A
~disp #0:20-30.A at n,c,o,h

Still one more step if you don’t want fake CA-CA bonds between adjacent residues for which you are showing sidechain only:

setattr m autochain false

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 11:21 AM, A G Szabo <agszabo at bell.net> wrote:

> Elaine
> 
> 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
> 
> arthur
> 
> -----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
> 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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