Hi Gerard Indeed. Calibration used to be part of the experiment, but it’s often forgotten these days (or it’s assumed that someone else has done it to an adequate standard - fortunately, this assumption is usually valid enough).
Harry > On 16 Jul 2020, at 12:37, Gerard Bricogne <g...@globalphasing.com> wrote: > > Dear Harry, > > I think that sharp ice rings (or, better, a powder pattern from silicon > powder) are only part of the solution to the calibration of beam energy, as > there is an interaction with the detector distance. If I recall what I saw > in my now distant days at LURE, a precise energy calibration would be done > using an absorption edge. I can remember Richard Kahn using a Cu metal foil > to lock precisely onto an energy close to the Ytterbium edge he wanted to > use in a MAD experiment. When the beam energy is precisely established by > this diffraction-free method, then a Si powder allows a precise calibration > of detector distance (and location of beam centre). > > > With best wishes, > > Gerard. > > -- > On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB 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/
