[phenixbb] treating the water molecules in the model

[Dmitry A. Semchonok]

Dear Pavel,

Thank you for your prompt response.

We will try and report back on results.

Just a small clarifying question -

> reference_coordinate_restraints.enabled=true
>
> reference_coordinate_restraints.selection=water
>
> reference_coordinate_restraints.sigma=0.2


I shall look and set in Real-space refinement protocol?


Many thanks.

Sincerely,
Dmitry

On January 20, 2024 5:25:24 AM Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Dmitry,
>
> Here are the considerations regarding water picking in cryo-EM maps:
>
> Unlike crystallography, where changing the model changes the maps (e.g., 
> adding more structure improves the maps), in cryo-EM, changing the model 
> does not change the map. Therefore, tasks such as refining B factors and 
> adding water are best done using the most complete and accurate atomic 
> model of the macromolecule, preferably towards the end.
>
>
> Once you have added water, you need to run a round of refinement and check 
> all water manually. While automated tools generally add water reasonably 
> well, there is no 100% guarantee that all water will be correct. Typically, 
> you perform this step once towards the end.
>
> "Flying water" seems to be an issue indeed. While I'm working on the 
> solution, a quick and easy workaround for you to use now is to restrain 
> water positions to their original coordinates using weak harmonic 
> restraints. Keywords you'll need:
>
> reference_coordinate_restraints.enabled=true
> reference_coordinate_restraints.selection=water
> reference_coordinate_restraints.sigma=0.2
>
> (also can be set up in the GUI).
>
> Let me know if you have any questions or need help!
>
> Good luck!
> Pavel
>
> On 1/19/24 03:33, Dmitry Semchonok wrote:
>> Dear colleagues,
>>
>>
>>
>> Please share your experience with how you handle the water molecules.
>>
>>
>>
>> So, we have a refined model and added the water molecules using the Douse 
>> protocol.  So, should we refine the model again afterwards? Or is the model 
>> considered ready?
>>
>>
>>
>> We tried to refine our model with water, but then the water molecules flew 
>> away from the places.
>>
>>
>>
>> Please let me know what is the correct way to proceed.
>>
>>
>>
>> Many thanks for considering my request.
>>
>>
>>
>> Sincerely,
>>
>> Dmitry
>>
>>
>>
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