[Chimera-users] Download specific chain only

Salam Al-Karadaghi salam.al-karadaghi at biochemistry.lu.se
Mon Feb 12 01:40:19 PST 2018

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,

On 11 feb. 2018, at 19:14, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Joe,
Eric also pointed out to me that it would be much easier to save the chain from ChimeraX than to text-edit the file.

In ChimeraX, you would just delete all the other chains and then save PDB, e.g. commands something like:

delete ~ /BB
save /Users/meng/Desktop/5iv5-bb.pdb

It seemed to work fine when I tried it!  Result attached.

> On Feb 11, 2018, at 10:04 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>> wrote:
> 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
> From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
> Sent: 11 February 2018 18:00:09
> To: Healey, Joe
> Cc: chimera-users at cgl.ucsf.edu<mailto: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:
> <Screen Shot 2018-02-11 at 9.58.04 AM.png>
> 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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