<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Bret,<br>
<br>
phenix.superpose_pdbs reports both rmsd values: before and after.
Also, if I remember correctly, it uses all matching atoms to
compute rmsd (and not only those used to perform superposition).
This may explain the difference. Also, it reports
rotation/translation matrices.<br>
<br>
More information:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/superpose_pdbs.htm">http://phenix-online.org/documentation/superpose_pdbs.htm</a><br>
<br>
Pavel<br>
<br>
On 4/4/13 7:00 AM, Bret Wallace wrote:<br>
</div>
<blockquote
cite="mid:CA+eJyhj49GiRNFSFZ4Ri+vOyYmeVGB0WrNjYj0pK=EPs=w3bnw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>Dear All,<br>
<br>
</div>
I have solved a complex structure of two proteins, and a
reviewer has asked to compare the altered interface binding of
one particular binding partner (protein2) in this complex to
various other similar deposited PDBs through r.m.s.d.
calculations and rotation/translation matrices.<br>
<br>
</div>
<div>After aligning ~4 structures from the PDB (specifically
aligning 1 chain to the other binding partner, protein1) to my
structure, I want to calculated the rmsd before and after
re-aligning the deposited structures (containing protein2) to
my complexed protein2.<br>
<br>
</div>
<div>I have used the superpose utility in phenix to align the
C-alphas, however, I am getting very large rmsd values after
alignment (~3.3). This is rather strange as the aligned
proteins are essentially the exact same, both in sequence and
secondary structure. Using various different programs such as
SSM, Coot, and others give me an rmsd value of ~1, which is
far more reasonable, but they do not output a "start" rmsd
value.<br>
<br>
</div>
<div>Any suggestions on what the cause of this large rmsd value?
Or possibly another program that could provide start and final
rmsd values along with rotation/translation matrices for
alignment?<br>
<br>
Thanks,<br>
Bret<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>