[phenixbb] RSRZ in Phenix?

Randy Read rjr27 at cam.ac.uk
Sun Dec 27 11:34:21 PST 2015

The argument for RSRZ last time we had the PDB X-ray validation task force was that it’s meant to be independent of resolution and residue type, i.e. if you’re trying to judge how well someone did in fitting a structure, you expect a much better CC for a Trp in a 1.8A resolution structure than you do for a Lys in a 2.8A resolution structure.  The RSRZ score compares the RSR for the residue type at its resolution with other residues of the same type at similar resolution.  (We used RSR because Gerard K had generated the statistics for that one and hadn’t done the same for RSCC, which may or may not have had advantages.)

However, it definitely has its problems.  For example, the RSRZ for a side chain in a 6A structure makes no sense whatsoever because, in order to get enough representatives of each residue type to generate statistics, you have to include all the structures from something like 3.5 to 8A resolution!  So we’re looking for better alternatives this time around in the VTF.  Suggestions with evidence are welcome!


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
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Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 27 Dec 2015, at 18:58, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Jacob,
> I'm surprised we actually output it somewhere. I'm yet to grasp its usefulness... For a local map quality measure a triplet of numbers {2mFo-DFc map value, mFo-DFc map value, CC} seem to be sufficient and have clearer intuitive meaning (to me at least), while if you name me a RSRZ value I would not be able to even guess if it is good, fair or poor. If you want it even more pedantic, then this is something you may consider
> http://journals.iucr.org/d/issues/2014/10/00/kw5094/kw5094.pdf
> Acta Cryst. (2014). D70, 2593–2606
> Pavel
> On 12/27/15 10:00, Keller, Jacob wrote:
>> Oops, sorry for the trouble--I seem to have found it in the "comprehensive validation" part (it's not a standard output from refinements, apparently.)
>> JPK
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Keller, Jacob
>> Sent: Sunday, December 27, 2015 12:56 PM
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] RSRZ in Phenix?
>> Dear Crystallographers,
>> Is there any place in Phenix where RSRZ or a similar measure is shown?
>> All the best,
>> Jacob Keller
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