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" To: "PHENIX user mailing list" 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

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Tom, no prob, i'll give it a try, thanks again! Nick ----- Original Message ----- From: "Tom Terwilliger" To: "PHENIX user mailing list" 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" To: "PHENIX user mailing list" 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

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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" To: "PHENIX user mailing list" 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" To: "PHENIX user mailing list" 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

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi Tom, we used to have this parameter (do_simulated_annealing under simulated annealing parameters scope), but it is gone while ago. To run SA in normal refinement you just say, for example: % phenix.refine l.mtz l.pdb main.simulated_annealing=true --overwrite Pavel. Thomas C. Terwilliger wrote:

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" To: "PHENIX user mailing list" 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" To: "PHENIX user mailing list" 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

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb