[Chimera-users] question

A G Szabo agszabo at bell.net
Tue Aug 11 10:06:58 PDT 2015

Today I was trying to Fetch 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 that there was no such file. The files come
from a paper by R M Voorhees, (2014) Cell 157:1632.

I went to the PDB website and was able to  access each of the files. So they
do exist.  However, when I tried to visualize them using Protein Workshop
the structure that appeared was a mixture of surfaces and ribbon structures.
I was not able  to do anything with any of the structures using 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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