I will refer you to a discussion we recently had on the CCP4BB on the same topic: <a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=CCP4BB&F=&S=&P=209060">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=CCP4BB&F=&S=&P=209060</a> <div>
<br></div><div><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=CCP4BB&F=&S=&P=209060"></a>My personal favorite is Profit (<a href="http://www.bioinf.org.uk/software/profit/index.html">http://www.bioinf.org.uk/software/profit/index.html</a>).<br>
<br><div class="gmail_quote">On Thu, Apr 8, 2010 at 11:19 AM, Young-Jin Cho <span dir="ltr"><<a href="mailto:yjcho@brandeis.edu">yjcho@brandeis.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Phenix users,<br>
I am wondering if phenix or other program provide superimposing pdb files as best as possible(!)<br>
I used Superpose in CCP4 but only worked for same sequence of pdb files.<br>
<br>
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.<br>
Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing.<br>
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?<br>
<br>
As always, thanks in advance,<br>
<br>
Young-Jin<br>
<br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>Jim Fairman, Ph D.<br>Post-Doctoral Fellow<br>National Institutes of Health - NIDDK<br>Cell: 1-865-748-8672<br>Lab: 1-301-594-9229<br>E-mail: <a href="mailto:fairman.jim@gmail.com">fairman.jim@gmail.com</a> <a href="mailto:james.fairman@nih.gov">james.fairman@nih.gov</a><br>
</div>