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