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<DIV><FONT face=Arial size=2>Pavel, how can I specify the request for averaged
Kick Maps on the command line , please?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Cheers,</FONT></DIV>
<DIV><FONT face=Arial size=2>Uli</FONT></DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=PAfonine@lbl.gov href="mailto:PAfonine@lbl.gov">Pavel Afonine</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=qunwan1@gmail.com
href="mailto:qunwan1@gmail.com">qunwan1@gmail.com</A> ; <A
title=phenixbb@phenix-online.org
href="mailto:phenixbb@phenix-online.org">PHENIX user mailing list</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, August 28, 2009 6:31
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [phenixbb] question about
composite SA_omit map in phenix</DIV>
<DIV><BR></DIV>Hi Qun Wan,<BR><BR>Alternatively, you can ask phenix.refine to
compute Average Kick Map, which is expected to be less biased or less noisy.
For more details about kick map, see recent publication:<BR><BR>Acta Cryst.
(2009). D65, 921-931.<BR><BR>Please let me know if you have
questions.<BR><BR>Pavel.<BR><BR><BR>On 8/28/09 7:52 AM, crystallogrphy wrote:
<BLOCKQUOTE
cite=mid:33fd30c80908280752q468277deidd9ed31e65f392c0@mail.gmail.com
type="cite">Hi, <BR>I am using molecular replacement to build a model
against a 2.2A resolution data set. However, the template model only has 23%
sequence identity. First, I use chainsaw in CCP4i to prune all side chain to
be poly-Ala except the identical residues. Then I use AutoMR and rigid body
refinement, I got Rfree=50%. The continuous electron density is not bad
showing second structures. However, the model has some out-of-registration
problem, for example, two proline are in a alpha-helix. In other words, it
has model bias. I want to use composite SA-omit to get a less model bias
map, not a simple composite omit map or a SA_omit map ommiting a part of the
region. <BR>Does someone know who to do this?<BR><BR>Thanks!<BR><BR>Qun
Wan<BR>postdoc fellow <BR>Case Western Reserve University<BR><PRE wrap=""><HR width="90%" SIZE=4>
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