One correction: Model should after molecular replacement and few cycles of refinement (perhaps with a little bir relaxed geometry, but not too much).
There is an option to use a model after molecular replacement but it is being migrated to another program that will have proper tests. Regards Garib > On 16 Jul 2020, at 22:34, Garib Murshudov <[email protected]> wrote: > > Hi Tim, > > There is an option to do unit cell parameter refinement (for all six > parameters in general which can only happen in P1). It is undocumented. > > Celrefine/lattice refine all # if you give scale instead of all then only one > parameter is refined. > > Cellrefine select <alpha>. # use only atomic B value < Bmedian + alpha * > Binterquartile_range > > > The last command was added to to reduce effect of wrong atoms. > > These command should enable refinement all parameters with due account for > symmetry. But I am worried about refinement of cell parameters using atomic > models. The problem is that it affects B values and I think if model is not > good then cells will be expanded to reduce non-bonding interactions. > I think it will give biased results. > For ideal case (when you deliberately change cell parameters) it worked > perfectly when I tried. However, for real cases I could not convince myself > to claim that it would give unbiased results. My current thought is that > either a model after molecular replacement should be used or cell parameters > should be refined outside using data only (then you can only make cell > parameters consistent with each other). > > If you still would want to use refmac to do this calculations then you should > do it iteratively. Refine cell, then change mtz file (different cell > parameters) then refine cell again. > Please also note that if you are refining cell parameters then the resolution > of the data will also change (if you are refining all six parameters then > changes will be anisotropic) > > > In general it is a trivial but extremely trivial problem. > > Regards > Garib > > > >> On 16 Jul 2020, at 18:31, Tim Gruene <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi Jessica, >> >> Jens Luebben wrote cellopt for this purpose. It is available from >> github, https://github.com/JLuebben/CellOpt >> <https://github.com/JLuebben/CellOpt> >> >> It is based on the idea available in whatcheck, i.e. to optimise the >> unit cell parameters based on geometry restraints DFIX/DANG. Those need >> to be three-dimensional: I've had cases where the restraints do not >> span all three dimensions. In this case one of the cell parameters can >> refine to unrealistic values. >> >> We are quite slow on the manuscript for its reference, but for the time >> being, please quote the nanoArgovia (www.nanoscience.ch >> <http://www.nanoscience.ch/>) project A12.01 >> (A3EDPI). >> >> cellopt is called liked a shelxl job, i.e. like 'cellopt name' where >> name.ins and name.hkl are present in the directory. You can add some >> constraints to the lattice type. >> >> Refmac5 can also refine the unit cell parameters (Max Clabbers has made >> use of this feature), but as far as I understand, refmac5 only scales >> the unit cell volume isotropically - I am happy to be corrected. >> >> When you resolution is quite high, say 0.7A like what we get for >> zeolites and some organic compounds, you can refine the cell and the >> distance simultaneously, only the BEAM correlates heavily with the >> distance. DIALS can produce plots for the correlation between refined >> parameters, which is very handy for electron diffraction data. >> >> Best wishes, >> Tim >> >> >> On Thu, 16 Jul 2020 >> 08:20:11 -0700 Jessica Bruhn >> <[email protected] >> <mailto:[email protected]>> wrote: >> >>> As someone working with continuous rotation electron diffraction, >>> mostly with small molecules, I am often very concerned about the >>> accuracy of my cell dimensions. I have to heavily restrain my >>> experimental geometry, including the detector distance, because they >>> are so unusual compared to X-ray setups. I also suspect that my >>> goniometer is less able to maintain a constant speed, resulting in >>> small errors in the oscillation per frame, especially for early and >>> late images. I have calibrated my microscope's camera length >>> (analogous to detector distance) with powder diffraction and even >>> include an elliptical distortion correction in DIALS, and I validated >>> my setup with some single crystal data. >>> >>> I am wondering if there is a way to refine my unit cell at the model >>> refinement step? Most of my structures are 0.9-1.1A and are refined in >>> SHELXL. I would think that refining my cell with the goal of bringing >>> my bond lengths closer to ideal lengths would be helpful. Is there a >>> way to do this? >>> >>> Best, >>> Jessica >>> >>> On Thu, Jul 16, 2020 at 7:36 AM Edward Snell <[email protected] >>> <mailto:[email protected]>> >>> wrote: >>> >>>> Not completely related to the question but at one particular >>>> European synchrotron there were a group of beamline scientists that >>>> also kept honey bees. The wax from each hive gave very beautiful >>>> powder diffraction patterns with the scattering being similar but >>>> distinctive to each hive. I was fortunate to observe this before my >>>> data collection - this was their calibration of the beam center. >>>> >>>> In the US, many years before BluIce there was a 'jiffy' software >>>> routine that would take a powder pattern and accurately calculate >>>> the beam center. This saved one of our structures. Wax, silicon >>>> powder, and other test samples were used. If I remember correctly >>>> cryo-vials had a powder signature and a magnet with part of a vial >>>> glued to it became part of the tool kit when one would still >>>> routinely travel to the beamline. >>>> >>>> I've been saved once with the powdered silicon. We had a hutch that >>>> was completely empty when we arrived due to an unanticipated >>>> emergency. A week of beamtime turned into an amazing educational >>>> opportunity to install and align the diffractometer. The powder >>>> data proved very useful in the energy calibration. After >>>> installation and alignment, unbelievably we were able to collect >>>> our data and get a publication from it. >>>> >>>> Best, >>>> >>>> Eddie >>>> >>>> Edward Snell Ph.D. >>>> >>>> Director of the NSF BioXFEL Science and Technology Center >>>> President and CEO Hauptman-Woodward Medical Research Institute >>>> BioInnovations Chaired Professorship, University at Buffalo, SUNY >>>> 700 Ellicott Street, Buffalo, NY 14203-1102 >>>> hwi.buffalo.edu <http://hwi.buffalo.edu/> >>>> Phone: (716) 898 8631 Fax: (716) 898 8660 >>>> Skype: eddie.snell Email: >>>> [email protected] Webpage: >>>> https://hwi.buffalo.edu/scientist-directory/snell/ >>>> >>>> >>>> -----Original Message----- >>>> From: CCP4 bulletin board [mailto:[email protected]] On Behalf >>>> Of Harry Powell - CCP4BB >>>> Sent: Thursday, July 16, 2020 7:26 AM >>>> To: [email protected] >>>> Subject: Re: [ccp4bb] Quote source inquiry >>>> >>>> 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 >>>>> <[email protected]> >>>> 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:[email protected] >>>>> ****************************************************************** >>>>> 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/ >>>> >>> >>> >> >> >> >> -- >> -- >> Tim Gruene >> Head of the Centre for X-ray Structure Analysis >> Faculty of Chemistry >> University of Vienna >> >> Phone: +43-1-4277-70202 >> >> GPG Key ID = A46BEE1A >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <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 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## 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/
