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CCP4BB  April 2012

CCP4BB April 2012

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Subject:

Re: "resolution" on PDB web page

From:

"Edward A. Berry" <[log in to unmask]>

Reply-To:

Edward A. Berry

Date:

Wed, 25 Apr 2012 09:55:17 -0400

Content-Type:

text/plain

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text/plain (72 lines)

We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.

As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.200
which should be the high resolution used in refinement.

I suppose in an "additional remark" you could give the
optical resolution or the resolution of 90% complete at I/sig=2.
Or the title could be "The 2.2A resolution structure of protein x",
never mind that there were a few reflections used at 1.7A.
eab

Mark J van Raaij wrote:
> Phoebe, Jan, PDB,
> is this something particular to the US portal of the PDB, or general?
> We always use the European portal pdbe and have not had such "problems".
> Mark
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
>
>
>
> On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:
>
>> There have been other manipulations with user-input values. We could not input solvent content 83% for 3cg8 (the real value!!!) as "being out of the allowed range".
>> The resulting value in the PDB is "NULL" not showing the actually interesting feature of the structure.
>>
>> I also noticed that the reported resolution values are nonsensically advertised with three decimal positions after the point which is not the way we would put it, is it?
>>
>> Either fight it or live with it ...
>>
>> Jan Dohnalek
>>
>>
>>
>>
>> On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice<[log in to unmask]>  wrote:
>> I just noticed that the PDB has changed the stated resolution for one of my old structures!  It was refined against a very anisotropic data set that extended to 2.2 in the best direction only.  When depositing I called the resolution 2.5 as a rough average of resolution in all 3 directions, but now PDB is advertising it as 2.2, which is misleading.
>>
>> I'm afraid I may not have paid enough attention to the fine print on this issue - is the PDB now automatically advertising the "resolution" of a structure as that of the outermost flyspeck used in refinement, regardless of more cautious assertions by the authors?  If so, I object!
>>
>> =====================================
>> Phoebe A. Rice
>> Dept. of Biochemistry&  Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>>
>>
>> --
>> Jan Dohnalek, Ph.D
>> Institute of Macromolecular Chemistry
>> Academy of Sciences of the Czech Republic
>> Heyrovskeho nam. 2
>> 16206 Praha 6
>> Czech Republic
>>
>> Tel: +420 296 809 340
>> Fax: +420 296 809 410
>

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