Maybe a silly question, but -
Is this "standard deviation of bond lengths" that of each bond type in
the Eng and Huber paper, or the standard deviations in the structure
being validated?
Robbie Joosten wrote:
> Note that we discuss rmsZ values in the paper, not rmsd. This is done on purpose; rmsd values do not take the standard
> deviation of bond lengths into account. This makes it needlessly difficult to compare values.
>
> Consider reporting rmsZ instead of rmsd.
>
> Cheers,
> Robbie
>
> Sent from my Windows Phone
> ------------------------------------------------------------------------------------------------------------------------
> From: Randy Read
> Sent: 2013-01-29 23:08
> To: [log in to unmask]
> Subject: Re: [ccp4bb] RMSD Citation
>
> Dear Peter,
>
> Shameless plug: you could do worse than to read the report of the X-ray Validation Task Force of the wwPDB
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195755/), which includes citations to the original literature such as the
> Engh & Huber studies on bond lengths and angles, and their standard deviations.
>
> Best wishes,
>
> Randy Read
>
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road E-mail: [log in to unmask]
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
> On 29 Jan 2013, at 20:47, Peter Randolph wrote:
>
>> My advisor has told me that an acceptable range for publication is an RMSD for bonds ~ 0.01 A and angles >2.0 degrees
> is acceptable for publication (with a proper R and R-free). Does anyone know where these values came from and if there a
> specific citation to go along with it?
>> Thanks,
>> Peter
>>
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