Re: [phenixbb] red blobs (Andrea Smith)

Hi Kay, I checked the log files and yes, it seems that it did the optimization: |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.10 Shrink truncation radius= 0.90                 | | all data:                         500 lowest resolution reflections:        | | r_work= 0.1640 r_free= 0.1843     r_work= 0.5012                            | |-----------------------------------------------------------------------------| r_solv=  0.00 r_shrink=  0.00 r_work=0.1971 r_free=0.2188 r_work_low=0.5809 r_solv=  0.10 r_shrink=  0.00 r_work=0.1912 r_free=0.2126 r_work_low=0.5665 r_solv=  0.20 r_shrink=  0.00 r_work=0.1846 r_free=0.2054 r_work_low=0.5571 r_solv=  0.30 r_shrink=  0.00 r_work=0.1780 r_free=0.1985 r_work_low=0.5402 ... Best, Andrea On Friday, March 15, 2024 09:01 CET, Kay Diederichs wrote:  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 This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".