I have a related question. Why calculating/reporting standard deviation for cell constants is not now mandatory in protein crystallography. Is there any reason for that (e.g. difficult to calculate or error in calculation). Now mmcif being the official format and there is mmcif category for esd, space should not be the issue.
Regards, Abhik On Thu, Jul 16, 2020 at 1:29 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You can change the cell dimensions without spoiling the map fit too much, > but obviously you need to convert deposited orthogonal coordinates back to > fractional using the given SCALEi matrix, than re-orthogonalise with the > modified cell.. > Eleanor > > On Thu, 16 Jul 2020 at 13:01, Schreuder, Herman /DE < > herman.schreu...@sanofi.com> wrote: > >> My guess is that the model no longer superimposed well onto the electron >> density map, which should be easy to spot. >> Best, >> Herman >> >> -----Ursprüngliche Nachricht----- >> Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Frances >> C. Bernstein >> Gesendet: Donnerstag, 16. Juli 2020 13:44 >> An: CCP4BB@JISCMAIL.AC.UK >> Betreff: [EXTERNAL] Re: [ccp4bb] Quote source inquiry >> >> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk >> >> >> >> I do not remember the date or the PDB entry but it was during the time >> that the PDB at BNL was including distance and angle outliers in the >> checking report sent back to the depositor. >> It was a not-too-large protein and there were perhaps half a dozen >> outliers each on distances and angles which was typical of an entry without >> 'problems'. So I sent the proposed entry to the depositor and got a >> panicked call that something was wrong based on the depositor looking at a >> display of the entry. By the next day the depositor had figured out that >> s/he had decided to convert to orthogonal for deposition and mistyped one >> of the cell dimensions by 1 Angstrom. That length was about 135 so the >> error was less than 1% in one direction and I was very impressed that the >> depositor had spotted it graphically. >> >> After I did the appropriate linear algebra to correct the coordinates I >> took a look at the distance and angle outliers. Of course they were >> different but to my great surprise there were about the same number of >> outliers for the 'bad' and the corrected entries. So based on the checking >> at that time we could not tell the bad from the good. >> >> I would be interested to know what would happen now with all the >> additional checking that is available. Perhaps someone should do that >> experiment. >> >> Frances >> >> ===================================================== >> **** Bernstein + Sons >> * * Information Systems Consultants >> **** 5 Brewster Lane, Bellport, NY 11713-2803 >> * * *** >> **** * Frances C. Bernstein >> * *** f...@bernstein-plus-sons.com >> *** * >> * *** 1-631-286-1339 FAX: 1-631-286-1999 >> ===================================================== >> >> On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote: >> >> > There was a case a few years ago (not too many though) where a 1.6 ? >> > 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 >> 1.6? >> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac. >> >> uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIBAg&c=Dbf9z >> >> oswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4 >> >> H8oHzZyRHMQu1AQ&m=neGK9dOkm8c1ZLG-f8T5L7zEiACrDM2eVYaJXmrkiRM&s=2K565 >> >> kF6vECVgdK3NW3IWs14rVR1jRCrWrMpobwoWM4&e= >> >> >> >> This message was issued to members of >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.u >> >> k_CCP4BB&d=DwIBAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK- >> >> CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=neGK9dOkm8c1ZLG-f8T5L7zEiA >> >> CrDM2eVYaJXmrkiRM&s=a3XS54tB48gb9BZh6M-dbk7FLBApEmBt_1IyJ0dWCTs&e=, a >> >> mailing list hosted by >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.u >> >> k&d=DwIBAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8C >> >> LLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=neGK9dOkm8c1ZLG-f8T5L7zEiACrDM2eV >> >> YaJXmrkiRM&s=jyBL_Zsty82nCN7fvDPaeu3ZgU7LP0cAmRtriN4nme4&e=, terms & >> >> conditions are available at >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac. >> >> uk_policyandsecurity_&d=DwIBAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcK >> >> l5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=neGK9dOkm8c1Z >> >> LG-f8T5L7zEiACrDM2eVYaJXmrkiRM&s=oGvA0cR7YOe93FGRvztvv5Wr8GRaLgBjYNRT >> >> A6XhAUE&e= >> >> >> > >> > >> > Best wishes, >> > >> > --Gerard >> > >> > ****************************************************************** >> > Gerard J. 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