Re: [ccp4bb] apologize

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CCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008

Previous message:
Subject: Re: crystallization robot
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-01-09

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Subject: Re: bond lengths, angles, ideality and refinements
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-01-09

Subject: Re: apologize
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2008-01-09

Check out the letters in the Dec 2007 edition of Acta D. There is
lively discussion even among the experts (and while I recall no
mention of angels in this discussion, there IS a reference to Winnie
the Pooh).

Acta Cryst. (2007). D63, 1274-1281
Acta Cryst. (2007). D63, 1282-1283

> Some people believe 0.02 Å deviation from ideality is reasonable,
> based on
> the accuracy of the dictionary values of bond lengths and angles;
> others
> consider that to be "too sloppy" and a way to artificially deflate
> Rfactors.
>
> I seem to have detected a tendency in the literature to aim for
> about 0.01
> Å deviation. The new refinement program phenix.refine, which is
> supposed
> to optimize weighting between X-ray terms and stereochemical
> constraints
> automatically, seems to settle in at quite conservative values,
> such as
> 0.005 Å, whereas with refmac, I can't seem to get the geometry any
> more
> ideal than 0.005 Å even if I try to idealize a structure in the
> absence of
> X-ray data.
>
> So, like you, I am a bit confused, and wouldn't mind hearing more
> from the
> experts.
>
> All the best,
>
> Bill
>
>
>
>
>
>
> yang li wrote:
>> Dear All,
>> I am very sorry to involve you into such insignificance
>> discussion,
>> I
>> have reached agreement
>> with Prof Gerard, please stop talking about things beyond science,
>> thanks!
>> I read a book today, which said "A refined model should
>> exhibit rms
>> deviations of no more
>> than 0.02A for bond length and 4 for bond angels", I just wonder
>> about the
>> standard of the
>> bond length and the bond angel. I think most of you have read similar
>> words!
>> But maybe I
>> didnot express clearly and made some phrasal mistakes.
>> At last, happy new year to you all--though very late!
>>
>>
>> Sincerely!
>> Yang Li
>>

------------------------------------------------------------------------
---------------
Patrick J. Loll, Ph. D. (215) 762-7706
Associate Professor FAX: (215) 762-4452
Department of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA

pat.loll@drexel.edu

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CCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008

Previous message:
Subject: Re: crystallization robot
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-01-09

Next message:
Subject: Re: bond lengths, angles, ideality and refinements
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-01-09