[Chimera-users] question

Conrad Huang conrad at cgl.ucsf.edu
Tue Aug 11 13:23:38 PDT 2015


Try fetching from the "PDB (mmCIF)" database instead of the plain "PDB". 
  The entries contain more than 100,000 atoms (>136,000 atoms for 3j7o), 
and the standard PDB format requires splitting the entry into multiple 
files.  mmCIF format does not have this limitation.

Chimera will probably be fairly slow in opening the files (a few 
minutes) and use up a lot of memory (~2GB on my Windows 10 machine), but 
3j7o opens for me.

Conrad

On 8/11/2015 10:06 AM, A G Szabo wrote:
> Today I was trying toFetch a series of files from the PDB. Their
> accession codes are 3J7O, 3J7Q, 3J7R, and 3J7P. These are structures of
> the ribosome complexed with a trimeric translocon, Sec61. Each time
> Chimera responded with an error message indicating thatthere was no such
> file. The files come from a paper byR M Voorhees, (2014) Cell 157:1632.
>
> I went to the PDB website and was able toaccess each of the files. So
> they do exist.  However, when I tried to visualize them using Protein
> Workshop the structure that appeared wasa mixture of surfaces and ribbon
> structures. I was not able  to do anything withany of thestructuresusing
> Protein Workshop. I could not delete any of the several components, nor
> change them to ribbon structures.
>
> I have been able to fetch,using Chimera,other PDB files that have the
> entire ribosome complexed with proteins of interest.
>
> I sent a message to PDB relating what I have encountered and am waiting
> for a response.
>
> My question to Chimera is to determine if there is a work around to get
> at any of these files.
>
> Thank you
>
> Arthur G.  Szabo
>
> Professor Emeritus Chemistry
>
> Wilfrid Laurier University
>
>
>
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