[phenixbb] how to move one domain of a protein in respect to another?

Pavel Afonine pafonine at lbl.gov
Wed Feb 9 13:05:03 PST 2011

  Hi Tatyana,

without knowing much details about how you want to move the domains I 
guess these tools may be handy:

phenix.pdbtools model.pdb rotate="10 20 30" translate="3 5 7"


phenix.superpose_pdbs pdb_file_fixed.pdb pdb_file_moving.pdb

and may be

phenix.pdbtools model.pdb --geometry-regularization


On 2/9/11 11:57 AM, Tatyana Sysoeva wrote:
> Dear all,
> I am working with a protein which form homooligomeric assembly. Each 
> subunit of the assembly consists of 2 subdomains. I would like to 
> create chimeras with the subdomains moved with respect to each other, 
> keeping the linkers.
> I am wondering what would be the easiest way to do this?
> Any suggestions are welcome!
> Sincerely,
> Tanya

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