[Chimera-users] needing help for separating structures

David Gae ddgae at ucdavis.edu
Mon Nov 26 11:13:38 PST 2018

Dear Yu,

Since I don’t know what S2 and S3 richer state is… I don’t know if this is going to help. 
but, you can open, select and save pdb chains in chimera command line and view only the selected subunits:

1) View only the selected chain
disp :.A-B

2) saving only selected PDB files 
open 6DHO 
select :.A-B
write selected 0 test.pdb 

then follow step 1.

if you don’t like cif file formats you can convert them in Phenix package (PDB tools).

Hope this helps,

> On Nov 24, 2018, at 11:28 AM, Yu Guo <yg2 at kth.se> wrote:
> Dear Sir/Madam,
>          I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY​ cluster and all its ligands? Thank you very much!
> Best wishes
> <6dho.cif>_______________________________________________
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