[phenixbb] red blobs (Andrea Smith)

[Andrea Smith]

Hi Kay,

I tried the mask optimization and there is no change in how the final map looks like.

Should I just make peace with it?

Best,
Andrea

On Thursday, March 14, 2024 23:11 CET, Kay Diederichs <kay.diederichs at uni-konstanz.de> wrote:
 Hi Andrea,

in your case, phenix.refine seems to fill bulk solvent into volumes that
are not actually filled by solvent.
It might help to optimize the mask, see
https://phenix-online.org/documentation/reference/refinement.html#bulk-solvent-correction-and-anisotropic-scaling
"6. Mask parameters".

Best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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