<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<META NAME="Generator" CONTENT="MS Exchange Server version 14.02.5004.000">
<TITLE>question</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/rtf format -->
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Today I was trying to</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">F</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">etch a series of files from the PDB. Their accession codes are 3</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">J</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">7O, 3J7Q, 3</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">J</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">7R</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">, and 3J7P. These are structures of the ribosome complexed with a trimeric translocon, Sec61. Each time Chimera responded with an error message indicating that</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">there was no such file. The files come from a paper by</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">R M Voorhees, (2014) Cell 157:1632.</FONT></SPAN><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I went to the PDB website and was able to</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri"> access each of the files. So they do exist. However, when I tried to visualize them using Protein Workshop the structure that appeared was</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">a mixture of surfaces and ribbon structures. I was not able to do anything with</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">any of the</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> stru</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">cture</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">s</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> using Protein Workshop. I could not delete any of the several components, nor change them to ribbon structures.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I have been able to fetch</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">,</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">using Chimera</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">,</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> other PDB files that have the entire ribosome complexed with proteins of interest.</FONT></SPAN><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I sent a message to PDB relating what I have encountered and am waiting for a response.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">My question to Chimera is to determine if there is a work around to get at any of these files.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Thank you</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Arthur G. Szabo</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Professor Emeritus Chemistry</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Wilfrid Laurier University</FONT></SPAN><SPAN LANG="en-ca"></SPAN></P>
</BODY>
</HTML>