Hi,

I went through the paper quickly during the day thinking I will have a thorough look at home only to realize I don't have acces to it.

From the quick look it seemed that my biological background will not be enough to understand all of it, but I remember that it said at the end that the mosaic model is implemented in phenix. However, I don't know where. I went through the parameters in GUI and didn't find anything that seemed to fit the description.

Could you please explain what setting I need to use in the refinement?

Thank you, best,
Andrea

On Friday, March 15, 2024 16:16 CET, Pavel Afonine <[email protected]> wrote:
 

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 <[email protected]>:
>
>> 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
>>> <[email protected]> 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: [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
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>>>> "smime.p7s".
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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".
>
>
>
>
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