Re: [ccp4bb] bond lengths, angles, ideality and refinements

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

Previous message:
Subject: Re: apologize
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-09

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Subject: Re: bond lengths, angles, ideality and refinements
From: Todd Holyoak tholyoak {- at -} KUMC {- dot -} EDU
Date: 2008-01-09

Subject: Re: bond lengths, angles, ideality and refinements
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-09

Sorry, that should have read

"because the value is established by social consensus, it is thus NOT
guaranteed to be perfectly accurate, ..."

In other words, one can imagine some source of systematic error in
establishing an ideal bond length. For example, the crystal packing
environment of small molecules might tend to distort a bond by a couple
hundredths of an Ångstrom.

William Scott wrote:
> Dear Yang Li:
>
>
> Happy New Year to you, too, (ahead of Feb. 7th).
>
> You certainly owe us no apology; the reverse may not be true.
>
> Your question is an important one, as is what you have written below.
>
> I'm not certain I have a completely satisfactory answer.
>
> The reason is that ideal bond lengths may or may not be "true" in the
> sense that the value is established by social consensus, and is thus
> guaranteed to be perfectly accurate, even though it may be quite precise.
>
> Because of this, and because of natural deviations from ideality (which
> really only become trustworthy observations at extremely high resolution),
> a certain amount of "wiggle room" is typically allowed in terms of rmsd.
>
> The more conservative the refinement, the smaller the rmsd from ideality
> will be.
>
> 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
>>
>

CCP4bb navigation

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

Previous message:
Subject: Re: apologize
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-09

Next message:
Subject: Re: bond lengths, angles, ideality and refinements
From: Todd Holyoak tholyoak {- at -} KUMC {- dot -} EDU
Date: 2008-01-09