B factor refinement in recent versions of phenix
Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine. The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A². So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8. I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab. Any ideas what might be causing this and how to revert to the original behavior? Thanks in advance Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app
Hi Oliver, can you try the latest Phenix: http://www.phenix-online.org/download/nightly_builds.cgi Let me know if this does not fix your problem. Pavel On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
Hello,
I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
Any ideas what might be causing this and how to revert to the original behavior?
Thanks in advance Oliver
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Oliver, p.s.: I see you actually tried one of the latest versions (I missed it in my previous reply). Can you try this: 1) reset all B-factors to average or simply used the model where B-factors are "nomral" (not "too" small); then 2) run phenix.refine with this model. If this does not help then please send me the inputs so I can reproduce this and see what's happening. Thanks, Pavel On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
Hello,
I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
Any ideas what might be causing this and how to revert to the original behavior?
Thanks in advance Oliver
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I was battling this same problem this morning, whereby the <B> of the structure is low and generating B-factors that are close to zero in many instances. This is at 2.6A where I don't generally expect issues with systematically low B-factors. Phil Jeffrey Princeton On 8/30/12 11:52 AM, Pavel Afonine wrote:
Hi Oliver,
p.s.: I see you actually tried one of the latest versions (I missed it in my previous reply). Can you try this:
1) reset all B-factors to average or simply used the model where B-factors are "nomral" (not "too" small); then 2) run phenix.refine with this model.
If this does not help then please send me the inputs so I can reproduce this and see what's happening.
Thanks, Pavel
On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
Hello,
I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
Any ideas what might be causing this and how to revert to the original behavior?
Thanks in advance Oliver
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Yes, I've had the same problem, too with two different structures. My solution to fix this is quite crude... before defining TLS groups, I remove 'zero' b-factors by hand (e.g. vi myfile.pdb searching /1.00 0.0 which gives all B-factors set to zero). This started when I upgraded to the latest phenix (1.8-1069), and going back in time, it doesn't seem to happen with 1.7 versions. Thanks for looking into this, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Phil Jeffrey [[email protected]] Sent: Thursday, August 30, 2012 12:39 PM To: PHENIX user mailing list Subject: Re: [phenixbb] B factor refinement in recent versions of phenix I was battling this same problem this morning, whereby the <B> of the structure is low and generating B-factors that are close to zero in many instances. This is at 2.6A where I don't generally expect issues with systematically low B-factors. Phil Jeffrey Princeton On 8/30/12 11:52 AM, Pavel Afonine wrote:
Hi Oliver,
p.s.: I see you actually tried one of the latest versions (I missed it in my previous reply). Can you try this:
1) reset all B-factors to average or simply used the model where B-factors are "nomral" (not "too" small); then 2) run phenix.refine with this model.
If this does not help then please send me the inputs so I can reproduce this and see what's happening.
Thanks, Pavel
On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
Hello,
I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
Any ideas what might be causing this and how to revert to the original behavior?
Thanks in advance Oliver
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi, this is just a summary.. In a nutshell the problem was following. Assuming total model structure factor is (for simplicity): Fmodel ~ exp(-Boverall_scale) * exp(-Batoms) it's clear that Boverall_scale and Batoms are correlated, and any combination of Boverall_scale and Batoms that maintains Boverall_scale+Batoms=const will not change the the total model structure factors (and therefore R-factors, etc). The new bulk-solvent and overall scaling algorithm that I switched to in April did not care about returning isotropic component of Boverall_scale back to atoms: http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf In fact (as explained above), the new algorithm does not use analytical form for overall scale at all. Therefore a portion of Batoms was systematically absorbed by Boverall_scale. Not sure if this is a real problem, but to be consistemt with previous versions and expectations, recently (may be a month ago or so) I changed it such that isotropic exponential component of overall scale is added back to atoms. So current version of phenix.refine should not produce these "too small" B-factors anymore. Anyone who experience this problem please try the latest Phenix from nightly builds: http://www.phenix-online.org/download/nightly_builds.cgi If this does not solve the problem please let me know. The most efficient way to let me know is to send me data and model files so I can reproduce and fix the problem. Thanks, Pavel On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
Hello,
I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
Any ideas what might be causing this and how to revert to the original behavior?
Thanks in advance Oliver
participants (4)
-
"Weiergräber, Oliver H." -
Gino Cingolani -
Pavel Afonine -
Phil Jeffrey