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. > > 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 > <https://secure-web.cisco.com/1N9RLqKadaEuTn9dklx-hZRSyXwWU5_s4Z71J9Ds8zeFoeI5zjdDYBjyvM1OhRmk1KkA_3CETaQYo0a5QP7nnS-UfPSiEBufn2fEAZragMXeIpVnXxrsu4nVWz1vrmf8A635wQpRPXo9AOxre3pPbfg9ENTLIZSUEO4ywwaR6yHuHxzAatHruFLHTUxblm7-2-64mt8V2BsuTfpwxUM6V7S5iCJbWmcHvUjuWYMuBk__lUTD00Jl4mXgVL77gW0Wfv7z3xkZYMJ9PTu8-p8VJKhf7mClgqKEdRe4KRs0rfZtZnraOBykXMIhWT7N60Ktypd2IEfFbQzpqg7HwfFF9yg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > > 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 this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://secure-web.cisco.com/1u9v1tS7ux9TmzfNVbpvN6bmQUtWV9nezgXf4sHUEGDjWFIJ_XIcvNNpI_8pi_1nAwX5JaBWM9q_U-Vm8MihhPprgdV1EKSYedlkPX5D7LfvCkGJ6n88QtfE62nrqZyOcmINli54GpA9DkLVvKOOT8QazBhYs17f6a31bz0oLjrJCSeTqq80PdpQ5UjK2sjktqsgpyLZlnTIyTzRQ5PuoanuOcN2X5IZ4gIyC3o0Fev2mltgwEkS-yacFa44lKxkHO8o7V4ObvncnTZBthteNzEet6oFs2fciJtj-bLT-dwSv8CMkCf5xecxTtOq9hykykkbnsLg1pxkBq4hS7UxT_w/https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1> > > 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 this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
