[phenixbb] red blobs (Andrea Smith)

[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 <kay.diederichs at uni-konstanz.de> 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
> <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

This e-mail is digitally signed. If your e-mail client does not have the
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