Hello Thripthi,
You can try PDBePISA for calculating the buried surface
area and interface area for the active site in your structure.
https://www.ebi.ac.uk/pdbe/pisa/
Regards
Ramanuj
To unsubscribe fr
Greetings! I am currently trying to find the surface area of a protein
active site. I tried with SASA but could not succeed. I wish to find the
area of ligand and the area in the active site it is binding to. I would
like to have some suggestions to proceed.
Thanking in advance,
Thripthi S.
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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
Sent: Monday, June 26, 2023 4:54 PM
To: De La
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
Thanks Eleanor.
Yes, only refine waters.
Best regards,
Pedro
From: Eleanor Dodson
Sent: Monday, June 26, 2023 4:42 PM
To: De La Torre Marquez, Pedro Luis
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Script to refine water molecules - help
External
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> wrote:
> Dear all,
>
> I hope everything is going well.
> Back in
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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