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<p style="margin-top:0;margin-bottom:0">Hi Elaine,</p>
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<p style="margin-top:0;margin-bottom:0">Yes thanks, I did also try it with ChimeraX, but couldn't figure out how (if it's possible) to re-save the chain only as a PDB.</p>
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</p>
<p style="margin-top:0;margin-bottom:0">I opted to download the mmCIF and text-parse in the end, which partially worked. I was able to parse out about half of the chains via BioPython, however it complained partway through that one of the chains is somehow
malformed, and I've not worked out what's happening yet!</p>
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<div>from Bio.PDB import MMCIFParser, PDBIO</div>
<div>import os, sys</div>
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<div>id = sys.argv[1]</div>
<div>cp = MMCIFParser()</div>
<div>io = PDBIO()</div>
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<div>cif = cp.get_structure(os.path.basename(sys.argv[1]), sys.argv[1])</div>
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</div>
<div>for chain in cif.get_chains():</div>
<div><span style="white-space:pre"></span>io.set_structure(chain)</div>
<div><span style="white-space:pre"></span>io.save(os.path.basename(sys.argv[1]) + "_" + chain.get_id() + ".pdb")</div>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MSRB</span><br>
</div>
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<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: +44 (0) 7536 042620 | </span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a> | ORCID: <span>orcid.org/0000-0002-9569-6738</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 11 February 2018 18:00:09<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Download specific chain only</font>
<div> </div>
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<div style="word-wrap:break-word; line-break:after-white-space">Hi Joe,
<div class="">Chimera does not have PDB fetch limited to a specific chain, sorry.</div>
<div class=""><br class="">
<div class="">Depending on what you’re doing, you might want to try ChimeraX instead. It has much better performance on large systems.</div>
<div class=""><<a href="http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html" class="">http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html</a>></div>
<div class=""><br class="">
</div>
<div class="">On my laptop, “open 5iv5” in ChimeraX takes only a few seconds to download the file and then show the structure:</div>
<div class=""><img id="x_5BB5F3EF-9A7E-4999-B0E7-1237151F8A86" width="640" height="384" class="" src="cid:62B63CFA-97D5-40FA-A2B1-CEC576909046@gateway.sonic.net"></div>
<div class=""><br class="">
</div>
<div class="">The ChimeraX download page lists some of the major features that are still missing:</div>
<div class=""><<a href="http://www.rbvi.ucsf.edu/chimerax/download.html" class="">http://www.rbvi.ucsf.edu/chimerax/download.html</a>></div>
<div class=""><br class="">
</div>
<div class="">If you really only wanted that chain, however, you could just download the entire structure file directly from the PDB website (not involving Chimera), text-edit the file to only the chain of interest, and then open it in Chimera.</div>
<div class=""><br class="">
</div>
<div class="">I hope this helps,</div>
<div class="">Elaine<br class="">
<div class="">-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
</div>
<br class="">
<blockquote type="cite" class="">On Feb 11, 2018, at 6:21 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>> wrote:<br class="">
<br class="">
Hi again Chimera team,<br class="">
I need to download a chain from an enormous macromolecular complex as it's so large it actually crashes Chimera!<br class="">
Is it possible to do this directly in chimera somehow (downloading just that specific chain or chains? The fetch dialogue doesn't seem to like the typical underscore notation (e.g. 5IV5_BB )<br class="">
Thanks<br class="">
Joe<br class="">
</blockquote>
<br class="">
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