[Chimera-users] PDB splitting

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 30 11:39:51 PST 2011

On Nov 30, 2011, at 6:16 AM, Milen Raytchev wrote:

> Hi everyone,
> First, thank you Tom for redirecting me.
> I am trying to split a long single chain which is contained in a PDB
> file into several shorter chains, each to be contained in individual
> PDB files. I have tried Chimera (save as) and PDBEditor.jar software
> to do that but each approach messes the format somehow and I cannot
> use it in Chimera later (visualization suffers). Could you recommend
> me a way to do this splitting properly such that the PDB format is not
> messed up in the resultant 6 AAA domains and I can use the files
> further in Chimera. The file is attached if of any use.

Hi Milen,
	This seems to be pretty straightforward.  Maybe I'm missing something?  Anyway, open the structure in Chimera and using whatever means you are comfortable with, select each part you want separately saved in turn.  After selecting each, save that part in a file with File->Save PDB... and turning on the "Save selected atoms only" option.  One possible way to select parts is to bring up the sequence viewer (Favorites->Sequence) and drag the mouse across the residues you want to select.
	If you need to change the chain IDs, you could then open your saved files and use the Change Chain IDs tool (in the Structure Editing category, and only in the 1.6 daily build) to change them.
	If this is what you're already doing perhaps you could describe the problems you're having in a little more detail?  The files I saved using the approach above looked fine when I opened them again in Chimera.


	Eric Pettersen
	UCSF Computer Graphics Lab

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