Dear Garib,
thank you very much for the details! If everything goes to plan, we are
going to use the Dectris QUADRO in September(ish), ideally also with
some protein crystals. In ED, distance calibration is more difficult
than with X-rays because of instabilities in the lens system (at least
with the older instruments), and because I do not work with a parallel
beam, but focus the beam onto the detector surface. This is not a very
reproducible process. In those cases where I got high resolution data,
the cell is often quite stable, and the distance can vary by about 5%...
Best regards,
Tim
On Thu, 16 Jul 2020 23:21:54 +0100
Garib Murshudov <[log in to unmask]> wrote:
> One correction: Model should after molecular replacement and few
> cycles of refinement (perhaps with a little bir relaxed geometry, but
> not too much).
>
> There is an option to use a model after molecular replacement but it
> is being migrated to another program that will have proper tests.
>
> Regards
> Garib
>
>
> > On 16 Jul 2020, at 22:34, Garib Murshudov <[log in to unmask]>
> > wrote:
> >
> > Hi Tim,
> >
> > There is an option to do unit cell parameter refinement (for all
> > six parameters in general which can only happen in P1). It is
> > undocumented.
> >
> > Celrefine/lattice refine all # if you give scale instead of all
> > then only one parameter is refined.
> >
> > Cellrefine select <alpha>. # use only atomic B value < Bmedian +
> > alpha * Binterquartile_range
> >
> >
> > The last command was added to to reduce effect of wrong atoms.
> >
> > These command should enable refinement all parameters with due
> > account for symmetry. But I am worried about refinement of cell
> > parameters using atomic models. The problem is that it affects B
> > values and I think if model is not good then cells will be expanded
> > to reduce non-bonding interactions. I think it will give biased
> > results. For ideal case (when you deliberately change cell
> > parameters) it worked perfectly when I tried. However, for real
> > cases I could not convince myself to claim that it would give
> > unbiased results. My current thought is that either a model after
> > molecular replacement should be used or cell parameters should be
> > refined outside using data only (then you can only make cell
> > parameters consistent with each other).
> >
> > If you still would want to use refmac to do this calculations then
> > you should do it iteratively. Refine cell, then change mtz file
> > (different cell parameters) then refine cell again. Please also
> > note that if you are refining cell parameters then the resolution
> > of the data will also change (if you are refining all six
> > parameters then changes will be anisotropic)
> >
> >
> > In general it is a trivial but extremely trivial problem.
> >
> > Regards
> > Garib
> >
> >
> >
> >> On 16 Jul 2020, at 18:31, Tim Gruene <[log in to unmask]
> >> <mailto:[log in to unmask]>> wrote:
> >>
> >> Hi Jessica,
> >>
> >> Jens Luebben wrote cellopt for this purpose. It is available from
> >> github, https://github.com/JLuebben/CellOpt
> >> <https://github.com/JLuebben/CellOpt>
> >>
> >> It is based on the idea available in whatcheck, i.e. to optimise
> >> the unit cell parameters based on geometry restraints DFIX/DANG.
> >> Those need to be three-dimensional: I've had cases where the
> >> restraints do not span all three dimensions. In this case one of
> >> the cell parameters can refine to unrealistic values.
> >>
> >> We are quite slow on the manuscript for its reference, but for the
> >> time being, please quote the nanoArgovia (www.nanoscience.ch
> >> <http://www.nanoscience.ch/>) project A12.01 (A3EDPI).
> >>
> >> cellopt is called liked a shelxl job, i.e. like 'cellopt name'
> >> where name.ins and name.hkl are present in the directory. You can
> >> add some constraints to the lattice type.
> >>
> >> Refmac5 can also refine the unit cell parameters (Max Clabbers has
> >> made use of this feature), but as far as I understand, refmac5
> >> only scales the unit cell volume isotropically - I am happy to be
> >> corrected.
> >>
> >> When you resolution is quite high, say 0.7A like what we get for
> >> zeolites and some organic compounds, you can refine the cell and
> >> the distance simultaneously, only the BEAM correlates heavily with
> >> the distance. DIALS can produce plots for the correlation between
> >> refined parameters, which is very handy for electron diffraction
> >> data.
> >>
> >> Best wishes,
> >> Tim
> >>
> >>
> >> On Thu, 16 Jul 2020
> >> 08:20:11 -0700 Jessica Bruhn
> >> <[log in to unmask]
> >> <mailto:[log in to unmask]>> wrote:
> >>> 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
> >>> <[log in to unmask] <mailto:[log in to unmask]>> 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 <http://hwi.buffalo.edu/>
> >>>> Phone: (716) 898 8631 Fax: (716) 898 8660
> >>>> Skype: eddie.snell Email:
> >>>> [log in to unmask] Webpage:
> >>>> https://hwi.buffalo.edu/scientist-directory/snell/
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> >>>> Behalf Of Harry Powell - CCP4BB
> >>>> Sent: Thursday, July 16, 2020 7:26 AM
> >>>> To: [log in to unmask]
> >>>> 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
> >>>>> <[log in to unmask]>
> >>>> 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
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> >>>>>
> >>>>>
> >>>>> Best wishes,
> >>>>>
> >>>>> --Gerard
> >>>>>
> >>>>> ******************************************************************
> >>>>> Gerard J. Kleywegt
> >>>>>
> >>>>> http://xray.bmc.uu.se/gerard mailto:[log in to unmask]
> >>>>> ******************************************************************
> >>>>> 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 !
> >>>>> ******************************************************************
> >>>>>
> >>>>> ######################################################################
> >>>>> ##
> >>>>>
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> >>>
> >>>
> >>
> >>
> >>
> >> --
> >> --
> >> Tim Gruene
> >> Head of the Centre for X-ray Structure Analysis
> >> Faculty of Chemistry
> >> University of Vienna
> >>
> >> Phone: +43-1-4277-70202
> >>
> >> GPG Key ID = A46BEE1A
> >>
> >> ########################################################################
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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
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