[phenixbb] red blobs (Andrea Smith)

[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 
> <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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-- 
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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