<html>Hi Kay,<br /><br />I checked the log files and yes, it seems that it did the optimization:<br /><br />|-Mask optimization: start----------------------------------------------------|<br />| Solvent (probe) radius= 1.10 Shrink truncation radius= 0.90 |<br />| all data: 500 lowest resolution reflections: |<br />| r_work= 0.1640 r_free= 0.1843 r_work= 0.5012 |<br />|-----------------------------------------------------------------------------|<br /><br />r_solv= 0.00 r_shrink= 0.00 r_work=0.1971 r_free=0.2188 r_work_low=0.5809<br />r_solv= 0.10 r_shrink= 0.00 r_work=0.1912 r_free=0.2126 r_work_low=0.5665<br />r_solv= 0.20 r_shrink= 0.00 r_work=0.1846 r_free=0.2054 r_work_low=0.5571<br />r_solv= 0.30 r_shrink= 0.00 r_work=0.1780 r_free=0.1985 r_work_low=0.5402<br />...<br /><br />Best,<br />Andrea<br /><br /><br /><br />On Friday, March 15, 2024 09:01 CET, Kay Diederichs <kay.diederichs@uni-konstanz.de> wrote:<br /> <blockquote type="cite" cite="fbcfa46b-11bf-4015-94b6-b4420e4dc0d3@uni-konstanz.de">Hi Andrea,<br /><br />hmm, did phenix.refine actually use optimize_mask=true ?<br /><br />If you compare the logfiles of phenix.refine (for the default run with<br />opimize_mask=false, and the new run with optimize_mask=true)<br />side-by-side with xxdiff or vimdiff (yes this needs to be run from a<br />command-line) then there should be a difference.<br /><br />Making peace with the red blobs is somewhat unsatisfactory from a<br />technical viewpoint, but probably not relevant from a biological one.<br /><br />I'd guess that the authors of<br />https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would be<br />interested to look at your case ...<br /><br />Best wishes,<br />Kay<br /><br /><br />Am 15.03.24 um 08:27 schrieb Andrea Smith:<br />> Hi Kay,<br />><br />> I tried the mask optimization and there is no change in how the final<br />> map looks like.<br />><br />> Should I just make peace with it?<br />><br />> Best,<br />> Andrea<br />><br />> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs<br />> <kay.diederichs@uni-konstanz.de> wrote:<br />>> Hi Andrea,<br />>><br />>> in your case, phenix.refine seems to fill bulk solvent into volumes that<br />>> are not actually filled by solvent.<br />>> It might help to optimize the mask, see<br />>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solvent-correction-and-anisotropic-scaling<br />>> "6. Mask parameters".<br />>><br />>> Best,<br />>> Kay<br />>> --<br />>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de<br />>> email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049<br />>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz<br />>><br />>> This e-mail is digitally signed. If your e-mail client does not have the<br />>> necessary capabilities, just ignore the attached signature "smime.p7s".<br />>> _______________________________________________<br />>> phenixbb mailing list<br />>> phenixbb@phenix-online.org<br />>> http://phenix-online.org/mailman/listinfo/phenixbb<br />>> Unsubscribe: phenixbb-leave@phenix-online.org<br /><br />--<br />Kay Diederichs http://strucbio.biologie.uni-konstanz.de<br />email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049<br />Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz<br /><br />This e-mail is digitally signed. If your e-mail client does not have the<br />necessary capabilities, just ignore the attached signature "smime.p7s".</blockquote></html>