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

Oliv Eidam eidamo at blur.compbio.ucsf.edu
Wed Feb 27 10:44:19 PST 2013


I would like to continue the B-factor discussion started by Demetres D. 
Leonidas on Nov 2, 2012 on CCP4BB:

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.


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<pafonine at 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

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:eidamo at blur.compbio.ucsf.edu

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