[Chimera-users] Download specific chain only

Healey, Joe J.R.J.Healey at warwick.ac.uk
Sun Feb 11 10:04:10 PST 2018


Hi Elaine,


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.


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!


from Bio.PDB import MMCIFParser, PDBIO
import os, sys

id = sys.argv[1]
cp = MMCIFParser()
io = PDBIO()

cif = cp.get_structure(os.path.basename(sys.argv[1]), sys.argv[1])

for chain in cif.get_chains():
io.set_structure(chain)
io.save(os.path.basename(sys.argv[1]) + "_" + chain.get_id() + ".pdb")



Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 11 February 2018 18:00:09
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Download specific chain only

Hi Joe,
Chimera does not have PDB fetch limited to a specific chain, sorry.

Depending on what you’re doing, you might want to try ChimeraX instead. It has much better performance on large systems.
<http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>

On my laptop, “open 5iv5” in ChimeraX takes only a few seconds to download the file and then show the structure:
[cid:62B63CFA-97D5-40FA-A2B1-CEC576909046 at gateway.sonic.net]

The ChimeraX download page lists some of the major features that are still missing:
<http://www.rbvi.ucsf.edu/chimerax/download.html>

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.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 11, 2018, at 6:21 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>> wrote:

Hi again Chimera team,
I need to download a chain from an enormous macromolecular complex as it's so large it actually crashes Chimera!
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 )
Thanks
Joe

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