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/
