[chimerax-users] .pdb from Protein Data Bank has more chains than expected

[Elaine Meng]

Hi Phil,
 You don't need to attach the data if it's accessible from the PDB.  If you go to the RCSB page for this entry
<https://www.rcsb.org/structure/7FDL>

... and keep clicking through the different assemblies displayed  in the upper left  you eventually get to Asymmetric Unit which shows all the copies.  So the file contains all that just because it's all in the crystallographic asymmetric unit (the copies may have slightly different conformations from one another).  It is not something one would know a priori without reading the paper or looking at the data on the website.

Here is information about the asymmetric unit vs. biological assemblies at the RCSB PDB
<https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/missing-coordinates-and-biological-assemblies>

 OK back to ChimeraX:  You can hide or delete the part you don't want using basic command-line specifications, e.g.

hide ~/A,B

(hide atoms that are NOT chains A,B)

How to specify atoms, residues, chains in commands:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

...or if it is too hard to figure out or remember commands, you can do it with the menu

Actions... Atoms/Bonds... hide
Select... Chains... Transcription factor EGL1... A
Actions... Atoms/Bonds... show
Select... Chains... Transcription factor WER... B
Actions... Atoms/Bonds... show
Select... Clear

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

> On Nov 9, 2022, at 3:14 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Everyone,
> 
> I downloaded the 7FDL .pdb from the Protein Data Bank.  I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L).  I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein.  It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment.
> 
> Two questions.  Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B.
> 
> I have attached the .pdb file.
> 
> Thanks for any advise.
> 
> Phil McClean
>