[phenixbb] red blobs (Andrea Smith)

Pavel Afonine pafonine at lbl.gov
Thu Mar 28 07:40:59 PDT 2024 

Hi Andrea,

here is what you can do today..

phenix.mosaic model.pdb data.mtz

(yes, command line only, so far).

This will take a minute or less (or more if the model is very large) and 
create model_mosaic.mtz file that contains the following Fourier map 
coefficients for mFo-DFc and 2mFo-DFc kind of maps:

mFo-DFc_whole
mFo-DFc_main
mFo-DFc_mosaic
2mFo-DFc_whole
2mFo-DFc_main
2mFo-DFc_mosaic

(you can see the MTZ file content by using this command: phenix.mtz.dump 
model_mosaic.mtz)

The suffixes 'whole', 'main' and 'mosaic' refer to the types of masks 
used in calculation of each map and are explained in the paper:

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

To reiterate:

'whole' refers to the standard default bulk-solvent mask;
'main' refers to the largest part of the standard default bulk-solvent 
mask (small mask droplets inside protein region are removed);
'mosaic' refers to the mosaic mask, which is essentially the 'main' mask 
plus only those smaller masks that contain measurable amounts of the 
bulk-solvent (the rest, empty ones, that are responsible for 'red blobs' 
are removed).

Next, you load these maps and your atomic model into Coot and inspect. 
Artifacts such as 'red blobs' you reported earlier should be absent in 
'mFo-DFc_mosaic' map. This may lead to improvement of corresponding 
'2mFo-DFc_mosaic' map.

Now, as you can see, this is separate from refinement.

Here is what you should be able to do tomorrow..

Today I will add a parameter to phenix.refine (main.mosaic=True/False), 
which means if you get and install tomorrow's nightly build of Phenix 
(dev-5285 and up) the mosaic maps, both mFo-DFc_main and 
2mFo-DFc_mosaic, will be present in the MTZ file created by 
phenix.refine (which is available in both CL and GUI).

Let me know if you have any questions!

Good luck!
Pavel


On 3/28/24 06:24, Andrea Smith wrote:
> Hi all,
>
> can anyone please tell me how to use the mosaic model? I went through 
> the phenix documentation and didn't find anything about how to use it.
>
> Thank you,
> Andrea
>
>
>
> On Friday, March 15, 2024 22:14 CET, "Andrea Smith" 
> <andrea.smith at uochb.cas.cz> wrote:
>> 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 <pafonine at lbl.gov> 
>> 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 <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
>>> >>>> have the
>>> >>>> necessary capabilities, just ignore the attached signature
>>> >>>> "smime.p7s".
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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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