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" <[email protected]>
To: "PHENIX user mailing list" <[email protected]>
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:[email protected]>[email protected]
www.noinaj.com
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected]
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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_______________________________________________
phenixbb mailing list
[email protected]
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: [email protected]
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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