[phenixbb] Superimposing homologues

Jonathan Elegheert jonathan.elegheert at ugent.be
Fri Apr 9 03:37:05 PDT 2010

Hi Young-Jin,

my personal favourite for superpositions is theseus3d 

It is Maximum Likelihood based and lets you do all the things you want, 
including the 'averaged structure' calculation.


Ghent University

Op 08/04/10 17:19, Young-Jin Cho schreef:
> 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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