Hi Oliv, this was discussed in the past indeed, and I believe I addressed the problem. So what you describe surprises me. To be on the same page, could you please send me the inputs necessary to reproduce the problem. Once I have the data I will have a look. Please send files to my email directly (not to the mailing list). 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