As someone working with continuous rotation electron diffraction, mostly with small molecules, I am often very concerned about the accuracy of my cell dimensions. I have to heavily restrain my experimental geometry, including the detector distance, because they are so unusual compared to X-ray setups. I also suspect that my goniometer is less able to maintain a constant speed, resulting in small errors in the oscillation per frame, especially for early and late images. I have calibrated my microscope's camera length (analogous to detector distance) with powder diffraction and even include an elliptical distortion correction in DIALS, and I validated my setup with some single crystal data.
I am wondering if there is a way to refine my unit cell at the model refinement step? Most of my structures are 0.9-1.1A and are refined in SHELXL. I would think that refining my cell with the goal of bringing my bond lengths closer to ideal lengths would be helpful. Is there a way to do this? Best, Jessica On Thu, Jul 16, 2020 at 7:36 AM Edward Snell <esn...@hwi.buffalo.edu> 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/ > -- Jessica Bruhn, Ph.D Principal Scientist NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com ######################################################################## 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/
