Re: [phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild
Hi Dale, Thanks for the notes! Here is what is supposed to happen: the autobuild wizard keeps all the data you supply. resolution=2.2 will set the resolution of model-building and density modification and refinement refinement_resolution=2.3 will set the resolution for refinement to 2.3 instead of the 2.2 defined by resolution=2.2 There is as you guessed a bug however somewhere in the communication between the autobuild wizard and phenix.refine, so the refinement_resolution did not get passed properly. I will fix that... Thanks! -Tom T . At 01:29 AM 12/17/2007, Dale Tronrud wrote:
The structure factors that I downloaded from the PDB for my little MR project contains both reflections behind the beam stop and reflections of higher resolution than even the original authors would use. When setting up the MR I entered the more restrictive resolution limits into the Wizard and Phaser appears to have obeyed.
As near as I can tell from the log files, however, Resolve is using all the data in the rebuild. I am including a copy of the log file from the "best" refinement. I would prefer that only data between 30 and 2.2A were used but it is clear that the refinement is, at least, monitoring the fit to all the data. I am presuming that the program is refining against the same data it is monitoring.
I would like to suggest that either the log file be clearer about the resolution limits it is actually refining to, or the plumbing that passes the resolution limits from the AutoMR wizard to the AutoBuild wizard be checked.
Dale Tronrud
P.S. That's all my problems... For now. The project I'm working on is cursed and brings out the worst in all the software I have used.
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://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
Dear Tom, Does this handle the inner resolution limit as well as the outer? Dale Tom Terwilliger wrote:
Hi Dale,
Thanks for the notes! Here is what is supposed to happen:
the autobuild wizard keeps all the data you supply. resolution=2.2 will set the resolution of model-building and density modification and refinement refinement_resolution=2.3 will set the resolution for refinement to 2.3 instead of the 2.2 defined by resolution=2.2
There is as you guessed a bug however somewhere in the communication between the autobuild wizard and phenix.refine, so the refinement_resolution did not get passed properly. I will fix that...
Thanks! -Tom T
. At 01:29 AM 12/17/2007, Dale Tronrud wrote:
The structure factors that I downloaded from the PDB for my little MR project contains both reflections behind the beam stop and reflections of higher resolution than even the original authors would use. When setting up the MR I entered the more restrictive resolution limits into the Wizard and Phaser appears to have obeyed.
As near as I can tell from the log files, however, Resolve is using all the data in the rebuild. I am including a copy of the log file from the "best" refinement. I would prefer that only data between 30 and 2.2A were used but it is clear that the refinement is, at least, monitoring the fit to all the data. I am presuming that the program is refining against the same data it is monitoring.
I would like to suggest that either the log file be clearer about the resolution limits it is actually refining to, or the plumbing that passes the resolution limits from the AutoMR wizard to the AutoBuild wizard be checked.
Dale Tronrud
P.S. That's all my problems... For now. The project I'm working on is cursed and brings out the worst in all the software I have used.
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://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Dale, You can set the inner resolution limit for density modification and model-building in autobuild with dmax=20. This is not handed to phenix.refine at present...I will add that. -Tom T At 11:46 AM 12/17/2007, you wrote:
Dear Tom,
Does this handle the inner resolution limit as well as the outer?
Dale
Tom Terwilliger wrote:
Hi Dale,
Thanks for the notes! Here is what is supposed to happen:
the autobuild wizard keeps all the data you supply. resolution=2.2 will set the resolution of model-building and density modification and refinement refinement_resolution=2.3 will set the resolution for refinement to 2.3 instead of the 2.2 defined by resolution=2.2
There is as you guessed a bug however somewhere in the communication between the autobuild wizard and phenix.refine, so the refinement_resolution did not get passed properly. I will fix that...
Thanks! -Tom T
. At 01:29 AM 12/17/2007, Dale Tronrud wrote:
The structure factors that I downloaded from the PDB for my little MR project contains both reflections behind the beam stop and reflections of higher resolution than even the original authors would use. When setting up the MR I entered the more restrictive resolution limits into the Wizard and Phaser appears to have obeyed.
As near as I can tell from the log files, however, Resolve is using all the data in the rebuild. I am including a copy of the log file from the "best" refinement. I would prefer that only data between 30 and 2.2A were used but it is clear that the refinement is, at least, monitoring the fit to all the data. I am presuming that the program is refining against the same data it is monitoring.
I would like to suggest that either the log file be clearer about the resolution limits it is actually refining to, or the plumbing that passes the resolution limits from the AutoMR wizard to the AutoBuild wizard be checked.
Dale Tronrud
P.S. That's all my problems... For now. The project I'm working on is cursed and brings out the worst in all the software I have used.
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://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
_______________________________________________ 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://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
participants (2)
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Dale Tronrud -
Tom Terwilliger