Hi Harry,
I laughed when I read your question below "Or is this considered just something
that old folk do?".
At the Australian Synchrotron MX beamlines (MX1 and MX2) we also go old-school
and collect Lanthanum hexaboride powder diffraction data during each user
setup. We collect a single 180 degree image of Lab6 at minimum detector
distance and then up to 500mm in 100mm steps. They we can analyse the data
(using automated fit2d scripts) to refine direct beam position on the detector
and the detector distance offset from reported distance. The lab6 pin is stored
in the robot dewar in a staff puck and mounting and collecting the 6-8 images
is quick (maybe 2 minutes?) as we have automated collection and processing that
runs via our user setup GUI.
This process means that values for distance and direct beam in the image
headers for each user experiment have been experimentally determined that
morning. This accuracy helps the reliability of our auto-processing (especially
for dodgy crystals). Energy is calibrated each user run or if the LaB6 data
suggests a change in "distance".
This is probably overkill but dates from the early days when we were building
user confidence in the beamlines. I also remember getting really frustrated in
the old days as a user with incorrect beam position and/or detector distance in
image headers and didn't want our users to have to deal with that. I also spent
many hours trying to refine beamX/Y from ice rings in imosflm from beamlines
with a postit-note stuck to the side of the monitor with cryptic beamX/Y values.
We do get teased by some of our beamline scientist colleagues for our very
extensive beamline setup for each user (we could probably go to monthly for
some checks and weekly for others) but it takes so little time to calibrate
using powder diffraction we have just kept doing it.
If you think that is not pedantic enough we also collect a full dataset of
cubic insulin for every setup and the user setup report shows the data
processing statistics (the users also get the raw data and auto-processing
files). If we cannot get really nice data (low Rmerge at low resolution and
good low res anomalous signal at 13keV on sulfur) on cubic insulin won't
release the beamline to users until we can investigate and fix the issue. It is
also quick as we have Eigers and collections are so fast now.
I guess it is just part of our user support philosophy. It can be so hard for
users to grow crystals and we want to make sure the data quality for our users
is the best possible. Most users don't get the attention to detail that goes on
"under the hood" at the beamlines and this is how it should be. It is our job
to handle that stuff and success means users just expect good data from good
crystals and they get it. If you don't look for problems in the beamlines you
don’t find them. I think lot of MX experiments are viable when a beamline has a
problem (fluctuating intensity, beam position vibration, structure in the beam
etc) but some experiments are more sensitive than others and users may think
they just have bad crystals despite pretty diffraction.
So yes, there are people these days who collect powder data for wavelength and
beam position reference.
Cheers,
Tom
On 16/7/20, 9:26 pm, "CCP4 bulletin board on behalf of Harry Powell - CCP4BB"
<CCP4BB@JISCMAIL.AC.UK on behalf of
0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> 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
>>
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>
>
> Best wishes,
>
> --Gerard
>
> ******************************************************************
> Gerard J. Kleywegt
>
> http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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