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

Hello, anyone who experienced similar problem please get next available nightly build version of Phenix (any version that is newer than today's one, which should be available in a day or a few days), and that should fix this problem. Please let me know otherwise. Pavel On 2/27/13 10:44 AM, Oliv Eidam wrote:

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