[phenixbb] s_annealing within AutoBUILD
Pavel Afonine
PAfonine at lbl.gov
Fri Jul 14 16:33:15 PDT 2006
Hi Tom,
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:
% phenix.refine l.mtz l.pdb main.simulated_annealing=true --overwrite
Pavel.
Thomas C. Terwilliger wrote:
>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 $PHENIX/phenix/phenix/autosol/run_phenix_refine.py at line
>144 from
> self.params.refinement.simulated_annealing.do_simulated_annealing=True
>
>to:
> self.params.refinement.main.simulated_annealing=True
>
>(don't change the indentation or anything, just the text).
>
>Ralf: can you possibly verify that this is the correct current syntax?
>
>This will in fact do SA refinement once per build cycle, just as you
>originally asked for.
>
>Thanks!
>-Tom T
>
>
>
>
>
>>Tom,
>>
>>made the changes to AutoBuild.py, works like a charm now! Thanks!
>>
>>
>>
>>cheers,
>>Nick
>>
>>
>>
>>
>>----- Original Message -----
>>From: "Tom Terwilliger" <terwilliger at lanl.gov>
>>To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
>>Sent: Friday, July 14, 2006 4:58 PM
>>Subject: Re: [phenixbb] s_annealing within AutoBUILD
>>
>>
>>
>>
>>>Hi Nick,
>>>
>>>Oops. I didn't recheck to make sure it comes up. It should have but
>>>doesn't. I left it off the menu I'm afraid.
>>>-Tom T
>>>
>>>ps. If you want to be adventurous, go to the file
>>>
>>>$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:
>>>
>>>
>>>>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" <terwilliger at lanl.gov>
>>>>To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
>>>>Sent: Friday, July 14, 2006 4:20 PM
>>>>Subject: Re: [phenixbb] s_annealing within AutoBUILD
>>>>
>>>>
>>>>
>>>>
>>>>>Hi Nick,
>>>>>
>>>>>Yes, you can modify the parameter "s_annealing" by going to the menu
>>>>>
>>>>>
>>>>at
>>>>
>>>>
>>>>>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
>>>>>
>>>>>
>>>>choose
>>>>
>>>>
>>>>>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:
>>>>>
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>
>>>>>>I am running AUTOBUILD on a friend's structure, and noticed in the
>>>>>>
>>>>>>
>>>>log
>>>>
>>>>
>>>>>>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
>>>>>>
>>>>>>
>>>>each
>>>>
>>>>
>>>>>>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
>>>>>><mailto:noinaj at uky.edu>noinaj at uky.edu
>>>>>>www.noinaj.com
>>>>>>
>>>>>>
>>>>>>_______________________________________________
>>>>>>phenixbb mailing list
>>>>>>phenixbb at phenix-online.org
>>>>>>http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>Thomas C. Terwilliger
>>>>>Mail Stop M888
>>>>>Los Alamos National Laboratory
>>>>>Los Alamos, NM 87545
>>>>>
>>>>>Tel: 505-667-0072 email: terwilliger at LANL.gov
>>>>>Fax: 505-665-3024 SOLVE web site:
>>>>>
>>>>>
>>>>http://solve.lanl.gov
>>>>
>>>>
>>>>>PHENIX web site: http:www.phenix-online.org
>>>>>ISFI Integrated Center for Structure and Function Innovation web
>>>>>
>>>>>
>>>>site:
>>>>
>>>>
>>>>>http://www.techcenter.mbi.ucla.edu
>>>>>TB Structural Genomics Consortium web site: http://www.tbgenomics.org
>>>>>
>>>>>_______________________________________________
>>>>>phenixbb mailing list
>>>>>phenixbb at phenix-online.org
>>>>>http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>
>>>>>
>>>>>
>>>>_______________________________________________
>>>>phenixbb mailing list
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>>>>
>>>>
>>>
>>>
>>>Thomas C. Terwilliger
>>>Mail Stop M888
>>>Los Alamos National Laboratory
>>>Los Alamos, NM 87545
>>>
>>>Tel: 505-667-0072 email: terwilliger at LANL.gov
>>>Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
>>>PHENIX web site: http:www.phenix-online.org
>>>ISFI Integrated Center for Structure and Function Innovation web site:
>>>http://www.techcenter.mbi.ucla.edu
>>>TB Structural Genomics Consortium web site: http://www.tbgenomics.org
>>>
>>>_______________________________________________
>>>phenixbb mailing list
>>>phenixbb at phenix-online.org
>>>http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>>
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>
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