John, I'm sure they were bred by Brother Adam! There is a nice paper on wax diffraction here:
https://fdocuments.net/document/crystallinity-of-plant-epicuticular-waxes-electron-and-x-ray-diffraction-studies.html There are others by the DLS team ;- Also, looks like the d-spacing was 3.72 Angstroms (not 2.72, sorry). Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com -------- Original Message -------- On 16 Jul 2020, 16:56, Jon Cooper wrote: > 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 ######################################################################## 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/
