[phenixbb] s_annealing within AutoBUILD

Nicholas Noinaj noinaj at uky.edu
Fri Jul 14 17:37:10 PDT 2006


Tom,

I know during the first build cycle, it worked.  Later on, I noticed that it reset s_annealing to false again, as you probably anticipated.  I will make the additional changes in the morning and let you know how it goes.  Thanks again!


Cheers,
Nick






-----Original Message-----
From: "Thomas C. Terwilliger" <terwilliger at lanl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Date: Fri, 14 Jul 2006 17:18:05 -0600 (MDT)
Subject: Re: [phenixbb] s_annealing within AutoBUILD

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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>>>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
>>
>
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________________________________________

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
noinaj at uky.edu
www.noinaj.com









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