[phenixbb] s_annealing within AutoBUILD

Peter Zwart PHZwart at lbl.gov
Fri Jul 14 14:35:46 PDT 2006


For those of you who are interested, I have placed a summary in the 
AutoBuild section of the (searchable!) phenix_wiki 
(http://www.phenix-online.org/phenix_wiki/):

http://www.phenix-online.org/phenix_wiki/AutoBuild

HTH

Peter





Noinaj wrote:
> 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
>>> 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
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb



More information about the phenixbb mailing list