I tested something similar as a postdoc with refinement of small molecules. At the time, I was interested in the contribution of ESD in cell parameters to the calculated ESD on bond lengths and angles following full-matrix least squares refinement in SHELXL. Indeed, the ESD on bonds and angles increased with an increase in ESD on cell parameters, so this topic is directly relevant for the subset of protein structures which diffract to very high resolution and are so laboriously refined. I didn't try the obvious extension of this which would be to artificially vary the small molecule cell dimensions and observe the outcomes on refinement statistics and ESDs, curious to know if anyone else has tried.
Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email [log in to unmask]
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Keller, Jacob
Sent: Tuesday, July 26, 2016 12:52 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Why don't we quote errors on unit cell constants in MX
I was surprised that Ethan's empirical experiment with cell parameter variation did not yield anything, but perhaps a more systematic minimization would yield something, especially, as I mentioned before, in the case of lower-res structures in which the cell parameter uncertainty would doubtless be far worse. Errors in cell parameters should be systematically stretching/shrinking the structure, albeit to a pretty small degree. Maybe the small degree would add up to a larger degree, however, when multiplied by 1000s of bond lengths/locations.
JPK
*******************************************
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus
email: [log in to unmask]
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________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Frank von Delft [[log in to unmask]]
Sent: Tuesday, July 26, 2016 12:41 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Why don't we quote errors on unit cell constants in MX
Angels on a pin...?
On 26/07/2016 17:37, Ethan Merritt wrote:
> On Tuesday, 26 July 2016 03:32:52 PM Thomas, Leonard M. wrote:
>> I have had this discussion with my small molecule colleague many times and have wondered myself why they are not reported. They are determined in HKL2000 and XDS, I don't recall if they are in moslfm and there is a mmCIF line for them. But once converted to an mtz they are basically ignored.
> The uncertainty in cell parameters determined by the data collection
> program is confounded by uncertainty in many other experimental
> parameters; notably wavelength and detector distance but also detector
> x/y positional readout accuracy. Worse yet, they may drift over the
> course of data collection (the wavelength certainly, but also the cell parameters themselves).
>
> This is largely masked by the discrete nature of the Bragg indices hkl.
> A 1% error in cell parameter or detector distance might prevent you
> from indexing the crystal at all, but it does not translate into
> uncertainty in the index values per se. That is, you don't get index
> uncertainties h = 1 ± 0.01, k = 2 ± .02 and so on.
> Instead an error in cell parameter or wavelength shows up in the
> calculated phases. But the uncertainty in phases is already large due
> to our imperfect models and the magnitude of this added error is tiny, albeit systematic.
>
> What would you do with such numbers if they were reported?
> I can imagine that recurring large errors on a particular beamline
> might indicate a fixable problem with the detector positioning or
> monochromator stability, but I am dubious it tells you anything about
> the reliability of structures determined from those data sets.
>
> Stepping back from theoretical arguments to anecdotal evidence...
> Years ago WHATIF used to (maybe still does?) analyze systematic
> deviation from ideal geometry in a refined model as a function of
> projection along the crystal axes, thereby suggesting an error in that cell parameter.
> But my experience has been that after changing the cell parameters
> accordingly, re-refining the structure, and re-analyzing in WHATIF the
> systematic deviation was only shifted, not improved.
> In my hands repeated cycles of cell parameter adjustment and
> re-refinement neither converged nor improved the overall model statistics.
> So I chalked this up as an interesting idea that didn't work out in
> practice, and I have not gone back to it since then.
>
> Ethan
>
>>
>> Leonard M. Thomas Ph.D.
>> Macromolecular Crystallography Laboratory Oklahoma COBRE in
>> Structural Biology Price Family Foundation Institute of Structural
>> Biology Department of Chemistry and Biochemistry University of
>> Oklahoma Stephenson Life Sciences Research Center
>> 101 Stephenson Parkway
>> Norman, OK 73019
>> 405-325-1126
>> [log in to unmask]
>> http://barlywine.chem.ou.edu
>> http://structuralbiology.ou.edu
>>
>> ________________________________________
>> From: CCP4 bulletin board <[log in to unmask]> on behalf of
>> Keller, Jacob <[log in to unmask]>
>> Sent: Tuesday, July 26, 2016 10:22:42 AM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Why don't we quote errors on unit cell
>> constants in MX
>>
>> I've wondered a couple of things on this score:
>>
>> --What is the general range in uncertainties of cell parameters? I assume there's a huge range as a function of resolution esp., but it would be nice to have a general feeling for it.
>>
>> --Has anyone experimented with implementing a cell parameter step in refinement? I would think the effect would be small but still perhaps significant, especially at lower resolution and/or when cell parameters are not known very precisely.
>>
>>
>> *******************************************
>> Jacob Pearson Keller, PhD
>> Research Scientist
>> HHMI Janelia Research Campus
>> email: [log in to unmask]
>> *******************************************
>>
>> ________________________________________
>> From: CCP4 bulletin board [[log in to unmask]] on behalf of Tim
>> Gruene [[log in to unmask]]
>> Sent: Tuesday, July 26, 2016 11:15 AM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Why don't we quote errors on unit cell
>> constants in MX
>>
>> Dear Graeme,
>>
>> XDS reports standard uncertainties of the unit cell parameters in
>> CORRECT.LP and I recently started to include this information in
>> publications. So at least one of us does ;-)
>>
>> I also include this information in the SHELXL ZERR keyword - as fas
>> as I understand it affects the s.u. for coordinates and other things
>> you can calculate with SHELXL.
>>
>> The information is not too obvious to access, and it only have
>> limited information content. Maybe that's why it isn't quoted.
>>
>> Best,
>> Tim
>>
>>
>> On Tuesday, July 26, 2016 03:07:03 PM Graeme Winter wrote:
>>> Dear CCP4BB
>>>
>>> Does anyone know why we don't quote standard uncertainties on unit
>>> cell constants in the way that the small molecule community do? It
>>> would seem in the new world of multi-crystal data sets and serial
>>> crystallography some idea of the measure of ignorance would be particularly valuable.
>>>
>>> I'm not worried about whether they are "right" or "true" just
>>> interested in why we don't quote them...
>>>
>>> An example for thaumatin may look like this, for example:
>>>
>>> Unit cell (with estimated std devs):
>>> 57.7841(1) 57.7841(1) 149.9963(3)
>>> 90.0000(0) 90.0000(0) 90.0000(0)
>>>
>>> (in other news, there is no place to store this information in an
>>> MTZ
>>> file...)
>>>
>>> Thanks & best wishes Graeme
>>>
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