Hi Gerard
Indeed. Calibration used to be part of the experiment, but it’s often forgotten these days (or it’s assumed that someone else has done it to an adequate standard - fortunately, this assumption is usually valid enough).
Harry
> On 16 Jul 2020, at 12:37, Gerard Bricogne <[log in to unmask]> wrote:
>
> Dear Harry,
>
> I think that sharp ice rings (or, better, a powder pattern from silicon
> powder) are only part of the solution to the calibration of beam energy, as
> there is an interaction with the detector distance. If I recall what I saw
> in my now distant days at LURE, a precise energy calibration would be done
> using an absorption edge. I can remember Richard Kahn using a Cu metal foil
> to lock precisely onto an energy close to the Ytterbium edge he wanted to
> use in a MAD experiment. When the beam energy is precisely established by
> this diffraction-free method, then a Si powder allows a precise calibration
> of detector distance (and location of beam centre).
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB 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 <[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 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:[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 !
>>> ******************************************************************
>>>
>>> ########################################################################
>>>
>>> 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/
|