[phenixbb] Superimposing homologues
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,
> phenixbb mailing list
> phenixbb at phenix-online.org
Jim Fairman, Ph D.
National Institutes of Health - NIDDK
E-mail: fairman.jim at gmail.com james.fairman at nih.gov
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