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<div class="">Hi,</div>
I am not really an expert, by I found it is possible to fetch a pdb file in Chimera, select one or more chains, delete them, and then do whatever you need on the remaining,
<div class="">Salam</div>
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<div class="">On 11 feb. 2018, at 19:14, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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<div class="PlainText">Hi Joe,<br class="">
Eric also pointed out to me that it would be much easier to save the chain from ChimeraX than to text-edit the file.<br class="">
<br class="">
In ChimeraX, you would just delete all the other chains and then save PDB, e.g. commands something like:<br class="">
<br class="">
delete ~ /BB<br class="">
save /Users/meng/Desktop/5iv5-bb.pdb<br class="">
<br class="">
It seemed to work fine when I tried it! Result attached.<br class="">
Elaine<br class="">
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> On Feb 11, 2018, at 10:04 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="">
><span class="Apple-converted-space"> </span><br class="">
> Hi Elaine,<br class="">
><span class="Apple-converted-space"> </span><br class="">
> 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.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> 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!<br class="">
><span class="Apple-converted-space"> </span><br class="">
> from Bio.PDB import MMCIFParser, PDBIO<br class="">
> import os, sys<br class="">
><span class="Apple-converted-space"> </span><br class="">
> id = sys.argv[1]<br class="">
> cp = MMCIFParser()<br class="">
> io = PDBIO()<br class="">
><span class="Apple-converted-space"> </span><br class="">
> cif = cp.get_structure(os.path.basename(sys.argv[1]), sys.argv[1])<br class="">
><span class="Apple-converted-space"> </span><br class="">
> for chain in cif.get_chains():<br class="">
> io.set_structure(chain)<br class="">
> io.save(os.path.basename(sys.argv[1]) + "_" + chain.get_id() + ".pdb")<br class="">
><span class="Apple-converted-space"> </span><br class="">
><span class="Apple-converted-space"> </span><br class="">
> Joe Healey<br class="">
><span class="Apple-converted-space"> </span><br class="">
> From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
> Sent: 11 February 2018 18:00:09<br class="">
> To: Healey, Joe<br class="">
> Cc:<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class="">
> Subject: Re: [Chimera-users] Download specific chain only<br class="">
> <span class="Apple-converted-space"> </span><br class="">
> Hi Joe,<br class="">
> Chimera does not have PDB fetch limited to a specific chain, sorry.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Depending on what you’re doing, you might want to try ChimeraX instead. It has much better performance on large systems.<br 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>><br class="">
><span class="Apple-converted-space"> </span><br class="">
> On my laptop, “open 5iv5” in ChimeraX takes only a few seconds to download the file and then show the structure:<br class="">
> <Screen Shot 2018-02-11 at 9.58.04 AM.png><br class="">
><span class="Apple-converted-space"> </span><br class="">
> The ChimeraX download page lists some of the major features that are still missing:<br class="">
> <<a href="http://www.rbvi.ucsf.edu/chimerax/download.html" class="">http://www.rbvi.ucsf.edu/chimerax/download.html</a>><br class="">
><span class="Apple-converted-space"> </span><br 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.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> I hope this helps,<br class="">
> Elaine<br class="">
> -----<br class="">
> Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br class="">
> UCSF Chimera(X) team<br class="">
> Department of Pharmaceutical Chemistry<br class="">
> University of California, San Francisco<br class="">
><span class="Apple-converted-space"> </span><br 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="">
>><span class="Apple-converted-space"> </span><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="">
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<span id="cid:A67ECB985692F64E8FC1C0D0C11DB38D@uw.lu.se"><5iv5-bb.pdb></span></div>
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