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Hi, <br><br>Thanks for answering my previous question about weight adjustment, but I have a new problem.<br>
<br>
If I use,<br>
<br>
ordered_solvent=true simulated_annealing=true \<br>
strategy=rigid_body+individual_sites+individual_adp \<br>
main.number_of_macro_cycles=10 \<br>
output.prefix=best_model --overwrite<br>
the program run fine and give the result: Start R-work = 0.4713, R-free = 0.4786, Final R-work = 0.2721, R-free = 0.3769<br>
<br>
<br>
However, when I tried to change weight,<br>
<br>
ordered_solvent=true simulated_annealing=true \<br>
strategy=rigid_body+individual_sites+individual_adp \<br>
optimize_wxu=true optimize_wxc=true \<br>
main.number_of_macro_cycles=10 \<br>
output.prefix=best_model --overwrite<br>
<br>
the program show error message, <br>
<br>
---------xray term weight optimization (wxc)---------- <br>
<br>
Traceback (most recent call last):<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module><br>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run<br>
call_back_after_monitor_collect=call_back_after_monitor_collect)<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run<br>
call_back_after_monitor_collect = call_back_after_monitor_collect)<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine<br>
log = log)<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__<br>
self.wxc_optimization()<br>
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization<br>
wxc = self.holder.wxc<br>
AttributeError: weight instance has no attribute 'holder'<br>
<br>
<br>
How do I fix this?<br><br><br>PC<br>
<br><br><hr id="stopSpelling">Date: Thu, 10 Dec 2009 08:31:25 -0800<br>From: PAfonine@lbl.gov<br>To: phenixbb@phenix-online.org<br>Subject: Re: [phenixbb] refinement<br><br>
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:
<blockquote cite="mid:SNT112-W65E022D2A8D5A9B30A685DB78D0@phx.gbl">
<style>
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</style>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="ecxstopSpelling">Date: Tue, 8 Dec 2009 20:12:29 -0800<br>
From: <a class="ecxmoz-txt-link-abbreviated" href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a><br>
To: <a class="ecxmoz-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:
<blockquote cite="mid:234998.1239.qm@web33308.mail.mud.yahoo.com">
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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>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br>
<div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2">
<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Ralf W. Grosse-Kunstleve <a class="ecxecxmoz-txt-link-rfc2396E" href="mailto:rwgk@cci.lbl.gov"><rwgk@cci.lbl.gov></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="ecxecxmoz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">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>
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