Re: [ccp4bb] an over refined structure

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Announcement: two crystallographic wikis
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-07

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Subject: Re: Different chains in the dimer
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-07

Subject: Re: an over refined structure
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-02-07

Dear CCP4ers,

I'm not convinced, that thin shells are sufficient: I think, in
principle, one should omit thick shells (greater than the diameter of
the G-function of the molecule/assembly that is used to describe NCS-
interactions in reciprocal space), and use the inner thin layer of
these thick shells, because only those should be completely
independent of any working set reflections. But this would be too
"expensive" given the low number of observed reflections that one
usually has ...
However, if you don't apply NCS restraints/constraints, there is no
need for any such precautions.

Best regards,

Dirk.

Am 07.02.2008 um 16:35 schrieb Doug Ohlendorf:

> It is important when using NCS that the Rfree reflections be
> selected is
> distributed thin resolution shells. That way application of NCS
> should not
> mix Rwork and Rfree sets. Normal random selection or Rfree + NCS
> (especially 4x or higher) will drive Rfree down unfairly.
>
> Doug Ohlendorf
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Eleanor Dodson
> Sent: Tuesday, February 05, 2008 3:38 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] an over refined structure
>
> I agree that the difference in Rwork to Rfree is quite acceptable at
> your resolution. You cannot/ should not use Rfactors as a criteria for
> structure correctness.
> As Ian points out - choosing a different Rfree set of reflections can
> change Rfree a good deal.
> certain NCS operators can relate reflections exactly making it hard to
> get a truly independent Free R set, and there are other reasons to
> make
> it a blunt edged tool.
>
> The map is the best validator - are there blobs still not fitted?
> (maybe
> side chains you have placed wrongly..) Are there many positive or
> negative peaks in the difference map? How well does the NCS match
> the 2
> molecules?
>
> etc etc.
> Eleanor
>
> George M. Sheldrick wrote:
>> Dear Sun,
>>
>> If we take Ian's formula for the ratio of R(free) to R(work) from his
>> paper Acta D56 (2000) 442-450 and make some reasonable
>> approximations,
>> we can reformulate it as:
>>
>> R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
>>
>> where s is the fractional solvent content, d is the resolution, p is
>> the effective number of parameters refined per atom after allowing
>> for
>> the restraints applied, d^3 means d cubed and sqrt means square root.
>>
>> The difficult number to estimate is p. It would be 4 for an isotropic
>> refinement without any restraints. I guess that p=1.5 might be an
>> appropriate value for a typical protein refinement (giving an R-
>> factor
>> ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor
>> ratio of 0.277/0.215 = 1.29 is well within the allowed range!
>>
>> However it should be added that this formula is almost a
>> self-fulfilling prophesy. If we relax the geometric restraints we
>> increase p, which then leads to a larger 'allowed' R-factor ratio!
>>
>> Best wishes, George
>>
>>
>> Prof. George M. Sheldrick FRS
>> Dept. Structural Chemistry,
>> University of Goettingen,
>> Tammannstr. 4,
>> D37077 Goettingen, Germany
>> Tel. +49-551-39-3021 or -3068
>> Fax. +49-551-39-2582
>>
>>
>>

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostrewa@lmb.uni-muenchen.de
*******************************************************

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Announcement: two crystallographic wikis
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-07

Next message:
Subject: Re: Different chains in the dimer
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-07