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
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From: Randy Read
Sent: 2013-01-29 23:08
To: [email protected]
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: [email protected]
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
