Maybe something is funny with my mtz? Dataset was processed with autoproc, then phaser and refinement in phenix...(1.21 I think) [image: image.png]
El lun, 20 may 2024 a la(s) 2:09 p.m., Eta Isiorho (eisio...@gc.cuny.edu) escribió: > In old coot ™, I leave the defaults alone when opening the 2Fo-Fc and > only check the box ‘assign labels…’ > > > > For the difference map, I change the amplitudes to ‘FOFC’ and the phases > to ‘PHFOFCWT’ and check the ‘assign labels’ box again along with the ‘is a > difference map’ > > > > This is the way I do it for my phenix outputs (the refmac output is > slightly different). > > > > The only time I see greyed out blocks for SIG Fobs and others, is when I > forget to press the ‘assign labels’ button for each map. > > > > > > *** > > Eta A. Isiorho, Ph.D. > Research Assistant Professor > Macromolecular Crystallization Facility Manager > CUNY Advanced Science Research Center > 85 Saint Nicholas Terrace, 3.352B/3.134 > New York, NY 10031 > eisio...@gc.cuny.edu > > > > > > *From: *Mailing list for users of COOT Crystallographic Software < > COOT@JISCMAIL.AC.UK> on behalf of Murpholino Peligro < > murpholi...@gmail.com> > *Date: *Monday, May 20, 2024 at 3:30 PM > *To: *COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> > *Subject: *Re: Updating maps > > ** This email originates from a sender outside of CUNY. Verify the sender > before replying or clicking on links and attachments. ** > > Dear Lucrezia and EE. > > > > When I open the mtz as suggested I get: > > > Amplitudes: ANOM_1, 2FOFCWT, 2FOFCWT_no_fill, FOFCWT and ANOM_2 > > Phases: PHIF-model(+), PHIF-model(-), PHANOM_1, PH2FOFCWT, > PH2FOFCWT_no_fill, PHFOFCWT and PANOM_2* > > ... > Assign Labels for Structure Factor Calculation? > > in new-coot: I cannot select anything (Fobs contains ANOM_1, Sig Fobs does > not have a thing, and R-free seems to have R-free-flags(+)) > > in old-coot: I can select stuff but I do not have F/SIGF, only have the > labels as above (ANOM_1, 2FOFCWT, 2FOFCWT_no_fill, FOFCWT and ANOM_2), SIG > Fobs is greyed out and R-free contains R-free-flags(+)) > > > > * It really says 'PANOM_2' > > phenix.mtz.dump says > phenix.mtz.dump b3x11_refine_006.mtz > Processing: b3x11_refine_006.mtz > Title: > /home/murphy/doc/phenix.refine/b3x11/truncate-unique.mtz:I(+),SIGI(+), > Space group symbol from file: P43212 > Space group number from file: 96 > Space group from matrices: P 43 21 2 (No. 96) > Point group symbol from file: 422 > Number of crystals: 2 > Number of Miller indices: 54730 > Resolution range: 55.5938 1.04901 > History: > Crystal 1: > Name: HKL_base > Project: HKL_base > Id: 0 > Unit cell: (78.6215, 78.6215, 37.0045, 90, 90, 90) > Number of datasets: 1 > Dataset 1: > Name: HKL_base > Id: 0 > Wavelength: 0 > Number of columns: 0 > Crystal 2: > Name: crystal > Project: project > Id: 2 > Unit cell: (78.6215, 78.6215, 37.0045, 90, 90, 90) > Number of datasets: 4 > Dataset 1: > Name: Original-experimental-data-mapped-to-asu > Id: 1 > Wavelength: 0.979 > Number of columns: 9 > label #valid %valid min max type > H 54730 100.00% 0.00 74.00 H: index h,k,l > K 54730 100.00% 0.00 52.00 H: index h,k,l > L 54730 100.00% 0.00 35.00 H: index h,k,l > I-obs(+) 47918 87.55% -8.88 9103.94 K: I(+) or I(-) > SIGI-obs(+) 47918 87.55% 0.19 1895.54 M: standard deviation > I-obs(-) 44308 80.96% -13.09 7510.68 K: I(+) or I(-) > SIGI-obs(-) 44308 80.96% 0.23 1895.11 M: standard deviation > R-free-flags(+) 54730 100.00% 0.00 19.00 I: integer > R-free-flags(-) 49051 89.62% 0.00 19.00 I: integer > Dataset 2: > Name: Experimental-data-used-in-refinement > Id: 2 > Wavelength: 0.979 > Number of columns: 4 > label #valid %valid min max type > F-obs-filtered(+) 47910 87.54% 1.97 888.48 G: F(+) or F(-) > SIGF-obs-filtered(+) 47910 87.54% 0.58 132.14 L: standard deviation > F-obs-filtered(-) 44300 80.94% 3.54 793.53 G: F(+) or F(-) > SIGF-obs-filtered(-) 44300 80.94% 1.30 140.15 L: standard deviation > Dataset 3: > Name: Model-structure-factors-(all-solvent-and-scales-included) > Id: 3 > Wavelength: 0.979 > Number of columns: 4 > label #valid %valid min max type > F-model(+) 47910 87.54% 0.01 1005.82 G: F(+) or F(-) > PHIF-model(+) 47910 87.54% -180.00 180.00 P: phase angle in degrees > F-model(-) 44300 80.94% 0.09 1005.82 G: F(+) or F(-) > PHIF-model(-) 44300 80.94% -179.98 179.98 P: phase angle in degrees > Dataset 4: > Name: Fourier-map-coefficients > Id: 4 > Wavelength: 0.979 > Number of columns: 10 > label #valid %valid min max type > ANOM_1 42215 77.13% 0.00 103.95 F: amplitude > PHANOM_1 42215 77.13% -179.98 180.00 P: phase angle in > degrees > 2FOFCWT 54718 99.98% 0.00 1559.94 F: amplitude > PH2FOFCWT 54718 99.98% -180.00 180.00 P: phase angle in > degrees > 2FOFCWT_no_fill 49995 91.35% 0.00 1139.40 F: amplitude > PH2FOFCWT_no_fill 49995 91.35% -180.00 180.00 P: phase angle in > degrees > FOFCWT 49995 91.35% 0.00 845.25 F: amplitude > PHFOFCWT 49995 91.35% -180.00 180.00 P: phase angle in > degrees > ANOM_2 42215 77.13% 0.00 103.95 F: amplitude > PANOM_2 42215 77.13% -179.98 180.00 P: phase angle in > degrees > > Thanks for your help > > > > > > El lun, 20 may 2024 a la(s) 8:58 a.m., Lucrezia Catapano ( > lucrezia.catap...@kcl.ac.uk) escribió: > > Dear Murpholino, > > > > The problem is the auto open MTZ. In your case the —auto option does not > assign F and SIGF. You need to use "open mtz" and assign them using the > option menu and the Rfree as well. > > > > Regards, > Lucrezia > > > > Sent from Outlook for iOS > <https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslO79Fy0g$> > ------------------------------ > > *From:* Mailing list for users of COOT Crystallographic Software < > COOT@JISCMAIL.AC.UK> on behalf of Murpholino Peligro < > murpholi...@gmail.com> > *Sent:* Monday, May 20, 2024 3:16:37 PM > *To:* COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> > *Subject:* Updating maps > > > > You don't often get email from murpholi...@gmail.com. Learn why this is > important > <https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslKpjcvEY$> > > How to Enable "Updating Maps"??? > > (Like the 2023 tutorial > <https://urldefense.com/v3/__https://pemsley.github.io/coot/blog/2023/05/05/coot-tutorial-in-2023.html__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslsvSzXYI$> > ) > > I tried enabling the option "updating maps" using the MTZ output from a > phenix.refine job with the following commands: > > > > cd Refine_6/ > > coot b3x11_refine_006.pdb --auto b3x11_refine_006.mtz > > After that, I went to Calculate -> Updating Maps, selected Auto Update, > and clicked OK. The labels were set to 2FOFCWT PH2FOFCWT, FOFCWT PHFOFCWT. > However, nothing happened—I could add or delete atoms, but there was no > change in the electron density maps. > > It works perfectly when using the tutorial "data". Why? Do I need > something else? > > PS. Trying in 'old-coot', but it would be good to know how to do this in > 'new-coot'. > > Thanks again! > > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslcTfO3Jw$> > > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslcTfO3Jw$> > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
