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 <eleanor.dod...@york.ac.uk>
Sent: Monday, June 26, 2023 4:54 PM
To: De La Torre Marquez, Pedro Luis <pedro_delatorremarq...@meei.harvard.edu>
Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@jiscmail.ac.uk>
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
<pedro_delatorremarq...@meei.harvard.edu<mailto:pedro_delatorremarq...@meei.harvard.edu>>
wrote:
Thanks Eleanor.
Yes, only refine waters.
Best regards,
Pedro
________________________________
From: Eleanor Dodson
<eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>>
Sent: Monday, June 26, 2023 4:42 PM
To: De La Torre Marquez, Pedro Luis
<pedro_delatorremarq...@meei.harvard.edu<mailto:pedro_delatorremarq...@meei.harvard.edu>>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
<CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>>
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
<pedro_delatorremarq...@meei.harvard.edu<mailto:pedro_delatorremarq...@meei.harvard.edu>>
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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