<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Tom,<br>
<br>
we used to have this parameter (do_simulated_annealing under simulated
annealing parameters scope), but it is gone while ago. To run SA in
normal refinement you just say, for example:<br>
<pre wrap="">% phenix.refine l.mtz l.pdb main.simulated_annealing=true --overwrite
Pavel.
</pre>
<br>
Thomas C. Terwilliger wrote:<br>
<blockquote
cite="mid56262.128.165.0.81.1152919085.squirrel@webmail.lanl.gov"
type="cite">
<pre wrap="">Hi Nick,
Great. In testing this, I found there is one more thing to do to make the
simulated annealing actually happen:
Edit the file $PHENIX/phenix/phenix/autosol/run_phenix_refine.py at line
144 from
self.params.refinement.simulated_annealing.do_simulated_annealing=True
to:
self.params.refinement.main.simulated_annealing=True
(don't change the indentation or anything, just the text).
Ralf: can you possibly verify that this is the correct current syntax?
This will in fact do SA refinement once per build cycle, just as you
originally asked for.
Thanks!
-Tom T
</pre>
<blockquote type="cite">
<pre wrap="">Tom,
made the changes to AutoBuild.py, works like a charm now! Thanks!
cheers,
Nick
----- Original Message -----
From: "Tom Terwilliger" <a class="moz-txt-link-rfc2396E" href="mailto:terwilliger@lanl.gov"><terwilliger@lanl.gov></a>
To: "PHENIX user mailing list" <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Sent: Friday, July 14, 2006 4:58 PM
Subject: Re: [phenixbb] s_annealing within AutoBUILD
</pre>
<blockquote type="cite">
<pre wrap="">Hi Nick,
Oops. I didn't recheck to make sure it comes up. It should have but
doesn't. I left it off the menu I'm afraid.
-Tom T
ps. If you want to be adventurous, go to the file
$PHENIX/phenix/phenix/wizards/AutoBuild.py
First copy the file to AutoBuild.py.orig to be safe, then
edit line 3342 from:
'start_chains_list','two_fofc_in_rebuild','input_labels',
to say instead
'start_chains_list','two_fofc_in_rebuild','input_labels','s_annealing',
and then close the wizard and open it again. This adds s_annealing to
the
menu and hopefully should cure the problem.
I'm sorry about that!
-Tom T
At 04:48 PM 7/14/2006 -0400, you wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Tom,
I thought that I just overlooked the s_annealing parameter, but this
doesn't seem to be the case. I don't seem to have this parameter in my
list. I am using the latest version of PHENIX loaded onto a LINUX
workstation.
Could it be that the parameter is missing or that I may have missed
something during the installation, since I am a newbie to Linux?
Thanks again in advance for all your help!
Cheers,
Nick
----- Original Message -----
From: "Tom Terwilliger" <a class="moz-txt-link-rfc2396E" href="mailto:terwilliger@lanl.gov"><terwilliger@lanl.gov></a>
To: "PHENIX user mailing list" <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Sent: Friday, July 14, 2006 4:20 PM
Subject: Re: [phenixbb] s_annealing within AutoBUILD
</pre>
<blockquote type="cite">
<pre wrap="">Hi Nick,
Yes, you can modify the parameter "s_annealing" by going to the menu
</pre>
</blockquote>
<pre wrap="">at
</pre>
<blockquote type="cite">
<pre wrap="">the
bottom right corner of the Parameters (inputs) screen labelled
SET VARIABLE (Advanced users)
and selecting "s_annealing"
then click "CONTINUE" and a screen will come up allowing you to
</pre>
</blockquote>
<pre wrap="">choose
</pre>
<blockquote type="cite">
<pre wrap="">Yes
or No to s_annealing. Then when you click CONTIUE the wizard will
continue
whatever it was doing.
You can set this variable when you are setting up your run; do it any
time
before the last screen comes up.
All the best,
Tom t
At 03:54 PM 7/14/2006 -0400, Noinaj wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I am running AUTOBUILD on a friend's structure, and noticed in the
</pre>
</blockquote>
</blockquote>
<pre wrap="">log
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">file the s_annealing parameter set to false. Is it possible to set
this
parameter to true when doing an AUTOBUILD run, say to do s_a after
</pre>
</blockquote>
</blockquote>
<pre wrap="">each
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">build cycle? I have read that I can use phenix.refine at the command
line
to run s_annealing, but didn't know if I could modify this option
within
the wizards. I checked out the list of parameters which I am allowed
to
change, but didn't see s_anneal anywhere.
Thanks for all replies in advance!
Cheers,
Nick
________________________________________
Nicholas Noinaj
University of Kentucky School of Medicine
Department of Molecular and Cellular Biochemistry
Biomedical Biological Sciences Research Building, Rm 236
741 S. Limestone
Lexington, Ky 40536
Lab: 859-323-8183
Home: 859-228-0978
<a class="moz-txt-link-rfc2396E" href="mailto:noinaj@uky.edu"><mailto:noinaj@uky.edu></a><a class="moz-txt-link-abbreviated" href="mailto:noinaj@uky.edu">noinaj@uky.edu</a>
<a class="moz-txt-link-abbreviated" href="http://www.noinaj.com">www.noinaj.com</a>
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<pre wrap="">
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: <a class="moz-txt-link-abbreviated" href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a>
Fax: 505-665-3024 SOLVE web site:
</pre>
</blockquote>
<pre wrap=""><a class="moz-txt-link-freetext" href="http://solve.lanl.gov">http://solve.lanl.gov</a>
</pre>
<blockquote type="cite">
<pre wrap="">PHENIX web site: <a class="moz-txt-link-freetext" href="http:www.phenix-online.org">http:www.phenix-online.org</a>
ISFI Integrated Center for Structure and Function Innovation web
</pre>
</blockquote>
<pre wrap="">site:
</pre>
<blockquote type="cite">
<pre wrap=""><a class="moz-txt-link-freetext" href="http://www.techcenter.mbi.ucla.edu">http://www.techcenter.mbi.ucla.edu</a>
TB Structural Genomics Consortium web site: <a class="moz-txt-link-freetext" href="http://www.tbgenomics.org">http://www.tbgenomics.org</a>
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<pre wrap="">
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: <a class="moz-txt-link-abbreviated" href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a>
Fax: 505-665-3024 SOLVE web site: <a class="moz-txt-link-freetext" href="http://solve.lanl.gov">http://solve.lanl.gov</a>
PHENIX web site: <a class="moz-txt-link-freetext" href="http:www.phenix-online.org">http:www.phenix-online.org</a>
ISFI Integrated Center for Structure and Function Innovation web site:
<a class="moz-txt-link-freetext" href="http://www.techcenter.mbi.ucla.edu">http://www.techcenter.mbi.ucla.edu</a>
TB Structural Genomics Consortium web site: <a class="moz-txt-link-freetext" href="http://www.tbgenomics.org">http://www.tbgenomics.org</a>
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>