Re: [ccp4bb] Script to refine water molecules - help

[De La Torre Marquez, Pedro Luis]

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 Torre Marquez, Pedro Luis 
Cc: 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 
mailto:pedro_delatorremarq...@meei.harvard.edu>>
 wrote:
Thanks Eleanor.

Yes, only refine waters.

Best regards,

Pedro

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Sent: Monday, June 26, 2023 4:42 PM
To: De La Torre Marquez, Pedro Luis 
mailto:pedro_delatorremarq...@meei.harvard.edu>>
Cc: CCP4BB@jiscmail.ac.uk<mailto: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 
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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Re: [ccp4bb] Script to refine water molecules - help

[De La Torre Marquez, Pedro Luis]

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 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 
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.

The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
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 .


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[ccp4bb] Script to refine water molecules - help

[De La Torre Marquez, Pedro Luis]

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.
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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[ccp4bb] CrystalEX 96 Well Flat Bottom Protein Crystallization Microplates from Corning (#3785D2) are out of stock

[De La Torre Marquez, Pedro Luis]

Hi,

I am Pedro and hope everything is going well.

I was using the CrystalEX 96 Well Flat Bottom Protein Crystallization 
Microplates from Corning (#3785D2) which is discontinued and out of stock. I am 
wondering if the best option as an alternative is the CrystalEX Second 
Generation Corning 3556 ? Any suggestions for another alternative from a 
different vendor?

Best regards,

Pedro.
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