That's interesting. I remember the days of wax rings, we even used to do several at different X-D distances. I sort-of lost faith with the advent of cryo since I had now idea of how this would affect the wax d-spacing (was it 2.72 Angstroms at rtp?) but ice-rings were always a life-saver to check the beam-centre. It would be interesting to know if 100K affects the wax d-value significantly. Another thing which slightly confused me is that it was popular belief that you could put the biggest piece of wax you could find in the beam. Maybe I missed something, but how is that ever going to give accurate X-D ;-?
With some structures, for the last round of refinement, I used to reprocess the data with XDS just to use the GLOREF option (sorry specialists!) which refined the cell with all the diffraction spots in the dataset, so as to get super-accurate cell dimensions for the last round. However, the last time I tried this, the GLOREF option had disappeared!! Perhaps there is an equivalent approach these days. Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com -------- Original Message -------- On 16 Jul 2020, 15:35, Edward Snell wrote: > Not completely related to the question but at one particular European > synchrotron there were a group of beamline scientists that also kept honey > bees. The wax from each hive gave very beautiful powder diffraction patterns > with the scattering being similar but distinctive to each hive. I was > fortunate to observe this before my data collection - this was their > calibration of the beam center. > > In the US, many years before BluIce there was a 'jiffy' software routine that > would take a powder pattern and accurately calculate the beam center. This > saved one of our structures. Wax, silicon powder, and other test samples were > used. If I remember correctly cryo-vials had a powder signature and a magnet > with part of a vial glued to it became part of the tool kit when one would > still routinely travel to the beamline. > > I've been saved once with the powdered silicon. We had a hutch that was > completely empty when we arrived due to an unanticipated emergency. A week of > beamtime turned into an amazing educational opportunity to install and align > the diffractometer. The powder data proved very useful in the energy > calibration. After installation and alignment, unbelievably we were able to > collect our data and get a publication from it. > > Best, > > Eddie > > Edward Snell Ph.D. > > Director of the NSF BioXFEL Science and Technology Center > President and CEO Hauptman-Woodward Medical Research Institute > BioInnovations Chaired Professorship, University at Buffalo, SUNY > 700 Ellicott Street, Buffalo, NY 14203-1102 > hwi.buffalo.edu > Phone: (716) 898 8631 Fax: (716) 898 8660 > Skype: eddie.snell Email: esn...@hwi.buffalo.edu > Webpage: https://hwi.buffalo.edu/scientist-directory/snell/ > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry > Powell - CCP4BB > Sent: Thursday, July 16, 2020 7:26 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > 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/ ######################################################################## 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/
