Hi, An alternative is to assess the quality of the phases (which are the result of the model refined against the data) via radiation-damage maps (what we call "F(early)-F(late) maps"). Assuming you collected high enough multiplicity data, autoPROC (which is what you used for processing, if I understood you right) would create those extra amplitudes in the output MTZ files if possible. Refinement with BUSTER would automatically compute and analyse those raditation damage maps for "interesting" sites, like decarboxylation, Cys-SG/Met-SD damage etc. You could then assume that the cleanest/strongest indications of such radiation damage arise when using the best phases (i.e. best model - as a result of best data to refine against).
For examples see e.g. https://www.globalphasing.com/buster/wiki/index.cgi?Covid19ReRefineRadDam https://www.globalphasing.com/buster/wiki/index.cgi?Covid19ReRefine5VZR and also https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg49077.html This would all be scriptable I guess. Cheers Clemens PS: there are only really two files coming out of autoPROC, namely truncate-unique.mtz (traditional, isotropic analysis) and staraniso_alldata-unique.mtz (anisotropic analysis via STARANISO). On Wed, Oct 27, 2021 at 12:58:53PM -0500, Murpholino Peligro wrote: > So... how can I get a metric for noise in electron density maps? > First thing that occurred to me > open in coot and do validate->difference map peaks-> get number of peaks > (is this scriptable?) > or > Second > phenix.real_space_correlation detail=residue file.pdb file.mtz > > > Thanks again > > El mié, 27 de oct. de 2021 a la(s) 10:52, vincent Chaptal ( > vincent.chap...@ibcp.fr) escribió: > > > Hi, > > > > It's hard to find a single metric... > > Ultimately, the quality of electron density maps, lower noise in fo-fc? > > > > Best > > Vincent > > > > Le 27/10/2021 à 17:44, Murpholino Peligro a écrit : > > > > Let's say I ran autoproc with different combinations of options for a > > specific dataset, producing dozens of different (but not so different) mtz > > files... > > Then I ran phenix.refine with the same options for the same structure but > > with all my mtz zoo > > What would be the best metric to say "hey this combo works the best!"? > > R-free? > > Thanks > > > > M. Peligro > > > > ------------------------------ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > -- > > > > Vincent Chaptal, PhD > > > > Director of GdR APPICOM > > > > Drug Resistance and Membrane Proteins Lab > > > > > > MMSB -UMR5086 > > > > 7 passage du Vercors > > > > 69007 LYON > > > > FRANCE > > > > +33 4 37 65 29 01 > > > > http://www.appicom.cnrs.fr > > > > http://mmsb.cnrs.fr/en/ > > > > > > > > ------------------------------ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
