[Chimera-users] PDB splitting

sette at uniroma2.it sette at uniroma2.it
Wed Nov 30 15:37:53 PST 2011


pdb files are text files so a text editor (cut and copy in a new file  
the region of interest) is a solution to the problem.


Eric Pettersen <pett at cgl.ucsf.edu> ha scritto:

> 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
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
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Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette at uniroma2.it
e-mail:        m77it at yahoo.it
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