Hi Edward It's the E & H value, i.e. the SU of the restraint, not that of the bond lengths & angles which in most cases is not calculated (you need to form the full Hessian matrix to do it).
The RMS Z-score doesn't behave as you might naively expect since you're actually comparing apples & pears, i.e. strictly the Z-score of any experimental observation is defined as the deviation of that observation from its expected value divided by the standard uncertainty of the deviation. In this case however the deviation is that of an observed bond length or angle from its expected value (i.e. the E & H value) divided by the SU of the E & H value, so it's not a true Z-score (let's call it a pseudo Z-score). Since the observed value is more or less correlated with the E & H value, dependent on the resolution (i.e. highly correlated at low resolution, less so at high res.), the E & H SU will always be an over-estimate of the true SU, hence the mean-square value of the pseudo Z-score will be smaller (by a factor that is resolution-dependent) than the expected mean-square value of a true Z-score (i.e. 1). Cheers -- Ian On 30 January 2013 22:37, Edward A. Berry <[email protected]> wrote: > 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: [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/<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 >>> >>>
