<div dir="ltr">I want to point out that this approach relies on consecutive residue numbering as a proxy for "no chain break." I've run into cases where this is not true - the main place this breaks down is with insertion codes. Alternate locations may also present challenges.<div><br></div><div>A more robust method would be to check that the coordinates of sequential CA atoms are within the expected distance.</div><div><br></div><div>For rolling one's own PDB parser, I'd recommend looking at the source code of Biopython's PDB parser for the column numbers that correspond to specific fields.</div><div><br></div><div>Cheers,</div><div><br></div><div>Lenna</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 10, 2015 at 8:46 PM, David Shin <span dir="ltr"><<a href="mailto:davidsshin@lbl.gov" target="_blank">davidsshin@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Patrick,<div><br></div><div>You should be able to write a script to do this (shell script with some python or awk).</div><div><br></div><div>Off the top of my head, for each file you would:</div><div><br></div><div>for each file:</div><div> extract the lines with ^ATOM into a new file to make things easier</div><div> read each line into some list</div><div> subtract the residue number from each line from the next line in the list</div><div> if that value is > 1 </div><div> print something ( the file name, or some flag)</div><div> else there are no breaks... can do something else if you want</div><div>end</div><div><br></div><div>The only tough parts are using spaces to separate items. If say a protein had 1000 residues, then the 1000 will run into the chain ID. So that's something to consider. Using specific column numbers would be the better way. </div><div><br></div><div>That and I'm not sure about the uniformity of PDB files that are really old.</div><div><br></div><div>Let me know if that helps, if not, I can maybe help out further.</div><div><br></div><div>Dave</div><div><br></div><div><br></div><div><br></div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">On Tue, Feb 10, 2015 at 2:24 PM, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Without manually checking every single one, there is no such list, at least that I know of. Your best bet could be to reduce your resolution as low as possible, usually those structures are of very good quality.</div><div><br></div><div>Cheers,</div><div><br></div><div>João</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-02-10 22:35 GMT+01:00 PC <span dir="ltr"><<a href="mailto:patrick.cossins@inbox.com" target="_blank">patrick.cossins@inbox.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I do know about PISCES lists but I want a list of PDB's without any chain breaks.<br>
<br>
Is there such a list or a way to obtain such a list?<br>
<br>
Thank you.<br>
<br>
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