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I also noticed a failure to converge when repeatedly re-refining a structure with cell parameters modified as suggested by WhatIf. The correction was always in the same direction, and about the same magnitude. I was told by someone (perhaps Gert Vriend himself?) that this was probably due to use of slightly different library values for bond lengths, in whatif vs xplr/cns. If that is the case it should be easy to fix. I think the values from structure refinement could well be more accurate than those from postrefinement, and at least they would be independent of errors in wavelength or camera length. eab On 07/26/2016 01:03 PM, Robbie Joosten wrote: > Hi Ethan, > > WHAT IF/ WHAT_CEHCK indeed still checks for systematic deviations in bond > lengths, but the output deformation matrix is not constrained to the space > group which doesn't make it easy to fix your cell dimensions. For refinement > I have seen some, but not a lot, effect when you change your cell dimensions > based on WHAT_CHECK's suggestions. This is partly due to the way I refine > models: refining for the best likelihood with reasonable bond length rmsZ, > gives enough slack to get good R-factors provided the cell dimensions are > not terribly far off. The low rmsd fetishists will benefit more from > correcting the cell dimensions because over-restraining your bond lengths > will lead to worse fit with the data. > > Cheers, > Robbie > >> -----Original Message----- >> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of >> Ethan Merritt >> Sent: Tuesday, July 26, 2016 18:38 >> To: [log in to unmask] >> Subject: Re: [ccp4bb] Why don't we quote errors on unit cell constants in > MX >> >> 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. 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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 >