[Chimera-users] secondary structure ribbons not drawn for CA-only protein

Arthur Szabo agszabo at outlook.com
Wed Aug 23 19:20:03 PDT 2017


Elaine 

Thank  you for your repl;y.

I found another structure that is complete 1GTR

Thanks for your information.


art

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, August 23, 2017 8:32 PM
To: Arthur Szabo <agszabo at outlook.com>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] secondary structure ribbons not drawn for CA-only protein

Hi Arthur,
PDB entry 1gsg contains only 1 atom per residue, CA atoms for the protein and P atoms for the tRNA.  Chimera does not draw the secondary-structure ribbons for alpha-carbon-only proteins because it uses the carbonyl oxygens to define the plane of the ribbon.  Some other program was used to make the image you see at the RCSB PDB.

You could instead try using some other structure that is more complete.  Here are all the structures with the same protein as 1gsg, most of which are complexed with tRNA (4jyz, 4jxx, etc.):
<http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=841BDC61>

I got this list by first searching RCSB PDB for 1GSG and going to its page:
<http://www.rcsb.org/pdb/explore/explore.do?structureId=1gsg>

… then lower in the page in the Macromolecules section, clicking the link to search for PDB structures with UniprotKB Access Code  “P00962”

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 23, 2017, at 4:03 PM, Arthur Szabo <agszabo at outlook.com> wrote:
> 
> I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with  the usual ribbon structure, bound to tRNA(Gln).
>  
> When I  fetch 1GSG using either the PDB file  number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or β-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition.  One can see the helical segments  in the worm like  structure, but not in the form of the usual helical secondary structure.
>  
> How can I  retrieve a structure that is  similar  to that in the PDB index list.
>  
> I have enclosed the following:
>  
> <image001.png>
>  
> This is  what comes up when I fetch the PDB file.
>  
> <image002.png>
>  
> Thanks
>  
> Arthur G. Szabo
> Professor Emeritus




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