[phenixbb] red blobs (Andrea Smith)

[Pavel Afonine]

Hi All,

The explanation of the reason for these blobs and the solution is both 
detailed in depth in this paper:

https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909

Quick facts are:

- These blobs are artifacts of bulk-solvent modeling.
- You can efficiently deal with them in Phenix.
- In some cases (which I witnessed myself), it is important to deal with 
them for map improvements elsewhere (for example, in regions of 
interest, such as ligands).

Let me know if you have any questions!

All the best,
Pavel


On 3/15/24 07:39, Mitchell D. Miller wrote:
> 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 <kay.diederichs at uni-konstanz.de>:
>
>> 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
>>>>
>>>> This e-mail is digitally signed. If your e-mail client does not 
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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
>> necessary capabilities, just ignore the attached signature "smime.p7s".
>
>
>
>
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