[phenixbb] Superimposing homologues

Jim Fairman fairman.jim at gmail.com
Thu Apr 8 08:30:51 PDT 2010

I will refer you to a discussion we recently had on the CCP4BB on the same

personal favorite is Profit (

On Thu, Apr 8, 2010 at 11:19 AM, Young-Jin Cho <yjcho at brandeis.edu> 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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Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman.jim at gmail.com james.fairman at nih.gov
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