[phenixbb] s_annealing within AutoBUILD

Noinaj noinaj at uky.edu
Fri Jul 14 14:18:49 PDT 2006


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
>> >
>> > _______________________________________________
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>> >
>>
>>_______________________________________________
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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
>
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