<html>Hi Kay,<br /><br />I tried the mask optimization and there is no change in how the final 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 <kay.diederichs@uni-konstanz.de> wrote:<br /> <blockquote type="cite" cite="2469f669-2218-4ffc-9212-7a7f74aed5d9@uni-konstanz.de">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</blockquote></html>