[phenixbb] Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)

Hi, I would like to continue the B-factor discussion started by Demetres D. Leonidas on Nov 2, 2012 on CCP4BB: http://www.mail-archive.com/[email protected]/msg29012.html I make the same observations like Demetres and Mingzhu Wang: unusually low B-factors when refining with Phenix 1.8-1069 and 1.8.1-1168, but not with Phenix 1.7.1-743. In numbers: the average B-factor is 10 A2 but it should be 20 A2 (based on Wilson B and similar structures). A few atoms (~20) have Bf = 0.00. The following is important: I refined dozens of similar structures without that problem and I observe this phenomenon only for a single data set. That specific data set is different because 1) I excluded regions with ice rings in XDS and 2) I limited the resolution to 2.28 Angstroem, although the crystal diffracted to ~1.8 Angstroem. While the preparation of the data set might be questionable in itself, I would prefer that this would not be the topic of this thread. My questions are: What can I do to refine my structure with Phenix 1.8.X using this truncated data set? What causes the difference in average B-factor values between Phenix 1.7 and 1.8 for this data set? Your advice is much appreciated. Oliv On 11/04/12 19:21, mingzhu wang wrote:

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:

...

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

-- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email:[email protected]