Re: [ccp4bb] unusually low B-factors
I think it may well be a problem with the scaling. It is hard to get a reasonable estimate of the Wilson B at 3A - especially in a small cell. Look at the Log Graph plots - one associated with R factor gives you Fobs and Fcalc v resolution. They SHOULD overlap pretty well, but sometimes they dont and sometimes that is because the OVERALL B is badly estimated. Of course it is a function of the data but often hard to correct.. Eleanor On 27 February 2014 16:26, Paul Paukstelis shocksofmig...@gmail.com wrote: Greetings, We've been working on a number of related structures. Crystals are in P64 with fairly small unit cell (40,40,55) and only diffract to around 2.5-3.0, so we aren't working with a lot of reflections. For several of these data sets the maps look very reasonable but Refmac refinement gives us unusually low B-factors after either individual or grouped refinement (average of around 10 A2 with some residues around 2 A2) while others are more 'normal' (avg. 30-40) with very similar maps. I suspect something in data processing, but I was wondering if there are opinions about what I should look for in cases like this. Thanks in advance. --paul
Re: [ccp4bb] Unusually low B factors with phenix
Pavel, 1.8.1-1168 also has this problem. I found this problem existed with some dataset, but not all dataset. 1.8.1 give better map, so I built model with 1.8.1 map and go back to 1.7.3 before I deposit the structure to PDB. When I compared the B factor from 1.8.x and 1.7.3, I found B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. 2012/11/3, Pavel Afonine pafon...@gmail.com: Joao, I am using the latest version of phenix 1.8.1-1168 1.8.1-1168 should not have that problem. If you suspect there is still a problem, you can send me the data and model files off list, explain what exactly the problem is, and I will have a look right away. FYI: there is Phenix mailing list for Phenix-specific questions, where I can also explain in great details the behavior with the B-factors you observe. All the best, Pavel
[ccp4bb] Unusually low B factors with phenix
Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Unusually low B factors with phenix
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE-
Re: [ccp4bb] Unusually low B factors with phenix
Dear Tim, this affects all atoms and yes I did reset the B-factors to 20.00 prior to refinement. I have not tried REFMAC but now I will give it a try since phenix does not seem to do the job. best Demetres On 2/11/2012 1:34 μμ, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE- -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Unusually low B factors with phenix
That sounds like the bug in Phenix.refine v1.8 that a few of us encountered - updating to the latest release will help. Actually wasn't so much a bug but a feature, albeit not the best one imaginable. Anyone using older v1.8 versions should update. --- Phil Jeffrey Princeton On Nov 2, 2012, at 6:41 AM, Demetres D. Leonidas ddleoni...@bio.uth.gr wrote: Dear Tim, this affects all atoms and yes I did reset the B-factors to 20.00 prior to refinement. I have not tried REFMAC but now I will give it a try since phenix does not seem to do the job. best Demetres On 2/11/2012 1:34 μμ, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE- -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Unusually low B factors with phenix
Joao, I am using the latest version of phenix 1.8.1-1168 1.8.1-1168 should not have that problem. If you suspect there is still a problem, you can send me the data and model files off list, explain what exactly the problem is, and I will have a look right away. FYI: there is Phenix mailing list for Phenix-specific questions, where I can also explain in great details the behavior with the B-factors you observe. All the best, Pavel
Re: [ccp4bb] Unusually low B factors after refinement
Hi Kyle, Are you refining with TLS? If so, then the default output will be the residual B-factors. To get the full B-factors you need to add the TLS component to the residual B's. This can be done by re-running your refmac job with the keyword TLSO ADDU Note that this version of refmac will also add your waters to TLS groups by default unless you give it the keyword TLSD waters Exclude So unless you included this keyword, then re-running refmac with your same input file and the TLSO ADDU keyword is the only way to ensure that your waters are converted to full B's as the CCP4 program TLSANL cannot do this since the TLS definitions in TLSOUT and the PDB header are not updated with regards to which waters were assigned to different TLS groups. Also, if you use the keyword TLSO ADDU, you should not use this PDB file as input to your next round of refinement unless you also use reset the B factors with the BFACtor SET ## keyword since refmac expects residual B's on the input file. I am not sure how many of these keywords are accessible via the ccp4i interface or if you have to add them via the run and view command file option if you use ccp4i. Regards, Mitch --- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kyle Dolan Sent: Friday, May 07, 2010 3:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusually low B factors after refinement Hello, I am trying to run restrained refinement with Refmac5 (version 5.5.0109), including refinement of isotropic temperature factors, and I am seeing some very unusual behavior by the program. In the output pdb file, nearly all of the individual atomic B factors have a value of 2.0! My data is only to 2.9 Angstrom so I've been told to expect much larger atomic B factors. I am using anisotropy-corrected data (I ran my original data through the ellipsoidal truncation anisotropy correction server from UCLA), but when I repeated the run using the original uncorrected mtz file I still saw an average atomic B around 10. I also looked back at the output pdbs from some previous rigid-body refinements (using the same anisotropy-corrected data) and there the B factors are much higher, 50-100. I'm not sure how to prevent Refmac from making this mistake--can anyone offer a suggestion? Thanks, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago k...@uchicago.edu
