July 2023 - phenixbb - phenix-online.org

map deposition strategy after density modification
by Daniel Larsson 20 Sep '23

20 Sep '23

Hi Phenix community, I’ve been using density modification with some success for my data and am considering the most appropriate way to do model building/refinement and then deposition of my results. Here are some questions/observations: 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one). 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map. 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs? 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps: "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect." But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right? 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one. So in conclusion, despite what I say above, the most conservative thing would be to deposit the conventionally sharpened map as my main map and use the original half-maps for calculating the FSC-curve and use the 0.143 threshold from this curve to estimate the resolution. The DM map can be used during rebuilding/refinement, but I think final minimization should be against the main map during deposition (with restraints if the geometry gets worse). The DM map can be deposited as an auxiliary map. Do the community and the developers agree? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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latest nightly build that runs on windows flawless
by Georg Mlynek 31 Jul '23

31 Jul '23

Hi community members, what is the latest latest nightly build that runs on windows flawless? I tried several versions after dev 4815 in the last year but all of them had different bugs. Most importantly the import of old projects should work. Many thanks, br Georg.

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General interest
by John R Helliwell 17 Jul '23

17 Jul '23

Dear Colleagues, I imagine that this book on the History of Scientific Journals: Publishing at The Royal Society 1665-2015, which I have reviewed in the current issue of J Appl Cryst will be of interest:- https://journals.iucr.org/j/issues/2023/04/00/xo0198/index.html My review is open access. The book itself is also open access:- https://www.jstor.org/stable/j.ctv2gz3zp1 Best wishes, John Emeritus Professor John R Helliwell DSc

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Phenix Phaser Question
by hyun4867 11 Jul '23

11 Jul '23

Dear, Everyone Hi all, I am Hyun Jeong. I want to ask you about phenix phaser problem. I obtain diffraction pattern of crystal that is complex. I tried to solve the phase based on the Apo structure i previoulsy solved. Using full-featured phaser, i obtain 18 Phaser solution. This is really strange number. But, the map obtained 18 Phaser solution is fitted in electron density map. May I proceed with processing using the discovered electron map with 18 Phasers? Is it necessary to redo the scaling? I appreciate your request for advice. Best regards, Hyun Jeong

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symmetry finding question
by Dmitry Semchonok 07 Jul '23

07 Jul '23

Dear colleagues, I have a chaperone map with D7 symmetry. But the Phenix «Map symmetry» tool finds only C7. Is there a way to make the software see the D7 symmetry of my protein? Many thanks for considering my request. Sincerely, Dmitry

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Discrepancy between Phenix GUI and command line for MR
by Xavier Brazzolotto 05 Jul '23

05 Jul '23

Dear Phenix users I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). Did you also observe such behavior? Best Xavier

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General interest, education article
by John R Helliwell 04 Jul '23

04 Jul '23

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