[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
> Eric Pettersen
> UCSF Computer Graphics Lab
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
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