Re: [phenixbb] red blobs (Andrea Smith)

Hi Andrea, You can also put a few zero occupancy atoms in the negative density to force phenix.refine to exclude the region from the bulk solvent mask. (You may also need to set refinement.mask.ignore_zero_occupancy_atoms = False so that the zero occupancy atoms are included in the mask) Regards, Mitch Quoting Kay Diederichs :

Hi Andrea,

hmm, did phenix.refine actually use optimize_mask=true ?

If you compare the logfiles of phenix.refine (for the default run with opimize_mask=false, and the new run with optimize_mask=true) side-by-side with xxdiff or vimdiff (yes this needs to be run from a command-line) then there should be a difference.

Making peace with the red blobs is somewhat unsatisfactory from a technical viewpoint, but probably not relevant from a biological one.

I'd guess that the authors of https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would be interested to look at your case ...

Best wishes, Kay

Am 15.03.24 um 08:27 schrieb 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 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-solve... "6. Mask parameters".

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

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

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