Indeed, centric reflections should have no anomalous signal after merging Phil
Sent from my iPhone > On 31 Mar 2020, at 05:48, Kevin Jude <[email protected]> wrote: > > > I've had two more helpful responses to this off-list. My crystal is P43212, > so there are large swaths of centric reflections that I was looking at. And > indeed, {18,1,1} is not the first reflection with anomalous differences if I > look more carefully. Different sorting of the outputs by phenix and aimless > masked that result for me. Thanks to those who responded for the help and for > the chance to dive into the International Tables. > > -- > Kevin Jude, PhD > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > >> On Mon, Mar 30, 2020 at 8:20 PM Kevin Jude <[email protected]> wrote: >> Thanks Reza. Changing the rejection criteria didn't have any effect, but I >> tried xdsconv and got what looked like the same result - ie, DANO = 0. That >> got me started looking at more reflections, and if I make it all the way >> down to {18,1,1) there's suddenly a switch and anomalous differences are >> present for the remaining reflections (which are sorted by increasing h, k, >> l). It turns out the same thing was happening in aimless. This seems strange >> since it isn't in accord with what I saw in CORRECT.LP, namely significant >> anomalous signal in the lower resolution shells, and it couldn't be >> explained away by a wedge of missing Friedel mates. >> >> Finally, I decided to see what happens if I used Phenix's reflection file >> editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine. >> So I suppose my problem of getting from here to there is solved, though the >> puzzle remains. >> >> -- >> Kevin Jude, PhD >> Structural Biology Research Specialist, Garcia Lab >> Howard Hughes Medical Institute >> Stanford University School of Medicine >> Beckman B177, 279 Campus Drive, Stanford CA 94305 >> Phone: (650) 723-6431 >> >> >>> On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim <[email protected]> wrote: >>> Hi Kevin, >>> Just a thought, guidance is left to the experts. Since the aimless reports >>> significant anomalous signal default anomalous rejection criteria most >>> likely is too strict for this run. Changing the default "reject 6 all -8" >>> value to loosen the rejection criteria might give some clue whether this is >>> the case. Another alternative is xdsconv. Any advantage of using pointless >>> and aimless instead of xdsconv for your purpose? >>> >>> Thanks, >>> Reza >>> >>> Md. Rezaul Karim (Reza) >>> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences >>> Department of Molecular Medicine >>> Morsani College of Medicine >>> University of South Florida >>> Schonbrunn lab, Moffitt Cancer Center >>> Tampa, FL >>> E-mail: [email protected], [email protected] >>> Phone: +1-954-937-8487 >>> ORCID: https://orcid.org/0000-0002-0424-127X >>> LinkedIn: https://www.linkedin.com/in/reza092 >>> >>> >>> >>> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude <[email protected]> >>> wrote: >>> >>> >>> Hi all, >>> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via >>> pointless and aimless. Everything looks good through pointless, as far as I >>> understand: >>> xds reports significant anomalous correlation in CORRECT.LP >>> >>> Inspection of the mtz output from pointless shows that (+) and (-) >>> reflections are recorded using separate ISYM flags (column 4): >>> >>> LIST OF REFLECTIONS >>> =================== >>> >>> 0 0 7 1 902 1.68 1.43 0.91 1230.80 >>> 1155.20 423.20 0.04 0.00 >>> >>> 0 0 7 2 2 1.21 1.68 0.90 1231.40 >>> 1155.10 243.20 0.04 0.00 >>> >>> 0 0 8 1 902 88.18 3.70 1.00 1230.70 >>> 1139.50 423.36 0.04 0.00 >>> >>> 0 0 8 2 2 85.93 3.86 0.99 1231.50 >>> 1139.30 243.36 0.04 0.00 >>> ... >>> >>> But when I run aimless as: >>> >>> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz >>> <<eof|tee aimless.log >>> onlymerge >>> anom on >>> reso 2.5 >>> end >>> eof >>> >>> the output mtz file has identical values for IMEAN, I(+), and I(-), despite >>> reporting in the logfile that: >>> Anomalous flag switched ON in input, strong anomalous signal found >>> Estimate of the resolution limit for a significant anomalous signal 3.93A, >>> from the point where the fit drops below threshold 0.15 >>> >>> Can anybody provide me with some guidance? >>> >>> Best wishes >>> Kevin >>> >>> -- >>> Kevin Jude, PhD >>> Structural Biology Research Specialist, Garcia Lab >>> Howard Hughes Medical Institute >>> Stanford University School of Medicine >>> Beckman B177, 279 Campus Drive, Stanford CA 94305 >>> Phone: (650) 723-6431 >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
