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
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright and or
> > privileged material, and are for the use of the intended addressee only. If
> > you are not the intended addressee or an authorised recipient of the
> > addressee please notify us of receipt by returning the e-mail and do not
> > use, copy, retain, distribute or disclose the information in or attached to
> > the e-mail. Any opinions expressed within this e-mail are those of the
> > individual and not necessarily of Diamond Light Source Ltd. Diamond Light
> > Source Ltd. cannot guarantee that this e-mail or any attachments are free
> > from viruses and we cannot accept liability for any damage which you may
> > sustain as a result of software viruses which may be transmitted in or with
> > the message. Diamond Light Source Limited (company no. 4375679). Registered
> > in England and Wales with its registered office at Diamond House, Harwell
> > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
> > Kingdom
> --
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
--
mail: Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
|