[phenixbb] Superimposing homologues

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Apr 8 08:33:49 PDT 2010

Hi  Young-Jin,

phenix.superpose_pdbs fixed.pdb moving.pdb

will do all these things for you except making the average structure.
All the best,
Tom T

>> 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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