The Coot API is quite useful for this sort of thing
imol = 0 # replace as needed
residues = residues_matching_criteria(imol, lambda chain_id, res_no,
ins_code, serial: residue_name(imol, chain_id, res_no, ins_code) == "HOH")
refine_residues(0, residues)
Regards,
Paul.
On 26/06/2023 22:14, De La Torre Marquez, Pedro Luis wrote:
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*[email protected].*
Dear Eleanor,
My apologies. Just to be more specific, I am just trying to run a Real
Space Refinement for the water molecules of my crystal structure with
COOT.
Thanks for all the help.
Pedro.
------------------------------------------------------------------------
*From:* Eleanor Dodson <[email protected]>
*Sent:* Monday, June 26, 2023 4:54 PM
*To:* De La Torre Marquez, Pedro Luis
<[email protected]>
*Cc:* [email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Script to refine water molecules - help
External Email - Use Caution
Wel - one way to do that is to use LABI FPART1=FS_from non-waters
PHIP1=PHIC_from non-waters.
You would need to split your model file into two - one containing the
atoms you want to fix, and the other the bits you want to refine.
Run 0 cycles of REFMAC to get an output with Fobs SIGFobs and FC PHIC
from the atoms you want to fix (0 cycles to prevent the protein moving
towards water positions)
Then refine the waters assigning LABI FP=..SIGFP=.. FPART1 and PHIP1
But I am not sure that is a very good idea? - there will be no
restraint terms between the atoms contributing to FPART and the waters
Good luck Eleanor
On Mon, 26 Jun 2023 at 21:44, De La Torre Marquez, Pedro Luis
<[email protected]> wrote:
Thanks Eleanor.
Yes, only refine waters.
Best regards,
Pedro
------------------------------------------------------------------------
*From:* Eleanor Dodson <[email protected]>
*Sent:* Monday, June 26, 2023 4:42 PM
*To:* De La Torre Marquez, Pedro Luis
<[email protected]>
*Cc:* [email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Script to refine water molecules - help
External Email - Use Caution
Do you mean only refine waters? In a general refinement run the
waters will be refined along with protin/ligands etc..
Eleanor
On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis
<[email protected]> wrote:
Dear all,
I hope everything is going well.
Back in 2019, I was using a script to refine all water
molecules automatically during the refinement of an X-ray
crystal structure. I no longer remember such script. Any
suggestion?
I will really appreciate it.
Pedro.
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