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<DIV><FONT face=Arial size=2>Hi Pavel,</FONT></DIV>
<DIV><FONT face=Arial size=2>Now that Randy sent you a reference about the
effect of very weak reflections will you include the changes in the
refiment procedure? </FONT></DIV>
<DIV><FONT face=Arial size=2>I am wondering about that because I get different
maps from the phenix refinement and from the refmac refinement. In one case I
see the isoalloxazine ring of the FAD cofactor flat, in the other case this ring
is bent. The same story with the densities for ligands. Is it about geometry
restraints or effects of exclusion of very weak reflections?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Maia</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<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=phenixbb@phenix-online.org
href="mailto:phenixbb@phenix-online.org">PHENIX user mailing list</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Thursday, December 10, 2009 9:31
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [phenixbb] refinement</DIV>
<DIV><BR></DIV>Hi Pei-Chun,<BR><BR>the target function for coordinates
refinement that is used in phenix.refine is following:<BR><BR>T = wxc_scale *
wxc * Txray + wc * Trestraints<BR><BR>where: wxc is determined automatically,
wc =1 by default, and wxc_scale = 0.5 by default. A user can adjust wxc_scale
or wc. <BR><BR>Responding your question about "put much more weight on
geometry restraints": you can do it either by decreasing wxc_scale or by
increasing wc. I would try an array of values for wxc_scale to see which one
gives the best result. <BR><BR>Please let me know if it's still not clear or
if you have any other questions!<BR><BR>Pavel.<BR><BR><BR>On 12/10/09 7:38 AM,
Pei-Chun Lin wrote:
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Hi, <BR><BR>When talking about "put much more weight on geometry restraints
to avoid overfitting", what wxc and wxu value will you suggest to use for a
4A structure?<BR>I am working on a 3.5A structure and have no experience of
adjusting weight value before. Any suggestion will be very helpful to
me.<BR><BR><BR>PC<BR><BR><BR>
<HR id=stopSpelling>
Date: Tue, 8 Dec 2009 20:12:29 -0800<BR>From: <A
class=moz-txt-link-abbreviated
href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</A><BR>To: <A
class=moz-txt-link-abbreviated
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A><BR>Subject:
Re: [phenixbb] refinement<BR><BR>Hi,<BR><BR>although I've seen cases like
yours when SA in Cartesian space did miracles, in many of cases modeling at
4A resolution is a tough problem. <BR><BR>Since clearly SA didn't work out
(given R/Rfree ~ 37/50% and the starting 48/50), I would try splitting your
model into rigid domains and refine each as a rigid body. Plus, I would
refine one isotropic B per residue or per domain (try both). This is a few
minutes to try so why don't you do so.<BR>Also, I would still combine it
(rigid body and B-factor refinement) with Cartesian SA, but I would put much
more weight on geometry restraints to avoid overfitting.<BR><BR>As you
probably aware of, in phenix.refine you can run combined refinement jobs,
for example, consisting of SA, rigid body, B-factor refinement and so on. So
I would recommend playing with the above suggestions to see if it works.
Plus, <B>don't forget looking at the maps - may be you manage to fit
something manually.</B><BR><BR>By the way, which R-factors you get if you
run:<BR><BR>phenix.model_vs_data data.mtz
model.pdb<BR><BR>(phenix.model_vs_data will account for twinning (if any)
using Xtriage automatically) ?<BR><BR>Write us if you have
questions.<BR><BR>Good luck,<BR>Pavel.<BR><BR><BR><BR>On 12/8/09 7:02 PM, r
n wrote:
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<DIV><SPAN style="FONT-FAMILY: tahoma,new york,times,serif">Thanks a
lot.<SPAN style="FONT-FAMILY: arial,helvetica,sans-serif"> I did download
the new -dev249 and did cartesian SA, R goes down to 37 but R-free (50)
did not. </SPAN></SPAN><BR>Any suggestions?<BR><BR><BR></DIV>
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style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman,new york,times,serif"><BR>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Ralf W.
Grosse-Kunstleve <A class=ecxmoz-txt-link-rfc2396E
href="mailto:rwgk@cci.lbl.gov"
moz-do-not-send="true"><rwgk@cci.lbl.gov></A><BR><B><SPAN
style="FONT-WEIGHT: bold">To:</SPAN></B> <A
class=ecxmoz-txt-link-abbreviated href="mailto:phenixbb@phenix-online.org"
moz-do-not-send="true">phenixbb@phenix-online.org</A><BR><B><SPAN
style="FONT-WEIGHT: bold">Sent:</SPAN></B> Tue, December 8, 2009 3:34:09
PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re:
[phenixbb] refinement<BR></FONT><BR>> I do have very low resolution
data (around 4 ang), what are<BR>> the efficient way of doing
refinement, either rigid body alone or<BR>> rigidbody and tls or
individual with group_adp. I did both, but not<BR>> much significant
changes in Rfree stays around 48/50%.<BR><BR>You could also try Cartesian
or torsion-angle simulated annealing.<BR>I'd try both. In my experience
Cartesian SA often works better even<BR>at low resolution.<BR>If you get
errors running torsion-angle annealing, please try<BR>the latest nightly
build (dev-249) since I've fixed several<BR>problems since the 1.5-2
release.<BR><BR>> Also I do have other questions<BR>>
<BR>> 1. While doing rigid body refinement, phenix complaint about
the<BR>> special position and could not perform rigid body
refinement,<BR>> whereas individual site refinement is working fine. I
do have to<BR>> delete the atom in special position for rigid body
refinement?<BR><BR>You could use<BR> sites.rigid_body = ...<BR>to
select the bodies you want to refine. The rest (including your<BR>atom on
the special position) will not
move.<BR><BR>Ralf<BR>_______________________________________________<BR>phenixbb
mailing list<BR><A href="mailto:phenixbb@phenix-online.org"
moz-do-not-send="true">phenixbb@phenix-online.org</A><BR><SPAN><A
href="http://phenix-online.org/mailman/listinfo/phenixbb"
moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/phenixbb</A></SPAN><BR></DIV></DIV></DIV><BR><PRE><HR width="90%" SIZE=4>
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