[phenixbb] s_annealing within AutoBUILD

Tom Terwilliger terwilliger at lanl.gov
Fri Jul 14 13:58:36 PDT 2006


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
> >
>
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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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