THis is always a difficult decision. More commonly I have worried about the best resolution cut off. Judge on high Rmerges? Keep the overall R value acceptably low?? etc etc..
I always come back to the map - is it sharper with the extra data? Is more unmodelled solvent showing up? etc.. But these decisions cannot be easily assessed by anyone else so I just keep as much information as I can , down to I/SigI ~ 1 , and let the R value climb.. However in the end it is a personal decision.. I wonder if the COOT validation of density fit could be used as a numerical tool.. What do you think Paul? Eleanor On Thu, 28 Oct 2021 at 08:46, Clemens Vonrhein <vonrh...@globalphasing.com> wrote: > 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/ > ######################################################################## 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/
