I think most of us are such "excellent" cryo-coolers that for every beamline shift we have multiple crystals with ice ring diffraction :-)
Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 16 Jul 2020, at 13:25, Harry Powell - CCP4BB > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Does anyone bother collecting a powder image (e.g. Si powder) these days so > they actually have a reference that can be used to check both the wavelength > and the beam centre? Or is this considered just something that old folk do? > > Harry > >> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt <ger...@xray.bmc.uu.se> wrote: >> >> There was a case a few years ago (not too many though) where a 1.6 Å >> structure had been solved using an incorrect value for the wavelength (~5% >> too low, leading to a cell that was slightly too small for its contents to >> be comfortable). It was later corrected so we could compare their validation >> statistics. Some interesting observations: >> >> - the geometry had been very tightly restrained so that didn't give a clue >> about the cell error (WhatCheck only suggested a very small change) >> >> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in >> the correct model (0.3% outliers in the wwPDB validation report), and the >> sidechain rotamer outliers even got worse (from 1.5 to 2.5 %) >> >> - the map looked surprisingly good for the incorrect cell >> >> - however, RSR-Z told clearly that the map was not good enough for the >> claimed >> resolution - the model had 24% outliers! (3% in the corrected model which >> still only put it at the ~50th percentile) >> >> - another good indicator was the clashscore (went from 44 to 7) >> >> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å >> resolution) ought to have provided a clue to the crystallographers and >> reviewers one would think >> >> It would be interesting to see what would happen if the wavelength would be >> set 5% too high. >> >> --Gerard >> >> >> >> On Thu, 16 Jul 2020, Clemens Vonrhein wrote: >> >>> Hi Robbie, >>> >>> On Wed, Jul 15, 2020 at 07:23:15PM +0000, Robbie Joosten wrote: >>>> At the same time if you have a a more relaxed approach to restraints >>>> than you might find systematic deviations in bond lengths. A test >>>> for that has been in WHAT_CHECK for decades and it actually works >>>> surprisingly well to detect cell dimension problems. >>> >>> Indeed. >>> >>>> That said, the problem is uncommon now. >>> >>> Not so sure about that: we all rely on an accurate value of the >>> energy/wavelength from the instrument/beamline - and if that is off >>> (for whatever reasons) it will result in incorrect cell dimensions and >>> a systematic deviation from the various restraints. >>> >>> This would even affect the best experiment done on the best crystal >>> ... so fairly easy to spot at the refinement stage, especially if such >>> an energy/wavelength offset is constant over a long period of time on >>> a given instrument. To spot this at the data collection stage one >>> would hope that at some point a crystal with very pronounced ice-rings >>> will be looked at properly (and the fact these are not where we expect >>> them to should cause some head-scratching). >>> >>> Cheers >>> >>> Clemens >>> >>> ######################################################################## >>> >>> 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/ >>> >> >> >> Best wishes, >> >> --Gerard >> >> ****************************************************************** >> Gerard J. Kleywegt >> >> http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se >> ****************************************************************** >> The opinions in this message are fictional. Any similarity >> to actual opinions, living or dead, is purely coincidental. >> ****************************************************************** >> Little known gastromathematical curiosity: let "z" be the >> radius and "a" the thickness of a pizza. Then the volume >> of that pizza is equal to pi*z*z*a ! >> ****************************************************************** >> >> ######################################################################## >> >> 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/ ######################################################################## 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/
