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
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
