[Chimera-users] Download specific chain only

Elaine Meng meng at cgl.ucsf.edu
Sun Feb 11 10:00:09 PST 2018


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:


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> 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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