[phenixbb] Superimposing homologues

Pavel Afonine PAfonine at lbl.gov
Thu Apr 8 08:36:14 PDT 2010

Hi Young-Jin,

yes, you can do it in PHENIX:

phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file]

More details:


Regarding your 3rd question: I'm not sure how you define an average 
structure. You need to define it first, then find out how to obtain it, 
and then you will be able to use the above tool

Let me know if you have questions.


On 4/8/10 8:19 AM, Young-Jin Cho wrote:
> Hi Phenix users,
> I am wondering if phenix or other program provide superimposing pdb files as best as possible(!)
> I used Superpose in CCP4 but only worked for same sequence of pdb files.
> So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job.
> Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing.
> Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison?
> As always, thanks in advance,
> Young-Jin
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