Hi Paul, For me, dummy waters are waters placed in very early models, where it is not yet clear whether the density belongs to a water, a rearranged side chain or a ligand. In the course of the refinement process, it becomes clear to which category the density really belongs. Especially for larger rebuilding, I find it helpful to use such waters.
A real water is for me a nicely defined, hydrogen bonded water in a well-refined structure. However, in this stage one does not need any RSR anymore. Best regards, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Paul Emsley Gesendet: Montag, 22. November 2021 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR What's the difference between a dummy water and a real one? Paul On 22/11/2021 14:34, Schreuder, Herman /DE wrote: Dear Paul, I agree with Oliver and Norbert, in the early phases of refinement, when a lot of rebuilding has to be done, the coot RSR is not very helpful and in general I leave it to buster do refine the rebuilt regions. Knowing now that (dummy) waters may be the culprit, I will remove them. However, it would be much more convenient if the repulsions with water molecules would not be taken into account. Thank you, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Norbert Straeter Gesendet: Sonntag, 21. November 2021 12:24 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: Re: [ccp4bb] COOT RSR Dear Paul, I agree to Oliver. In situations where you want to fit a "dummy water" to a difference density peak (to determine distances to the environment) or try the fit of solvent molecules to yet unexplained density, it would be nice to first obtain an optimal fit and next think about the environment and possible bumps and partial occupancy. I had this problem already several times, that I could not get a good fit because of the model repulsions. Even if two partially occupied waters are at closed distance the repulsions appear to be active in RSR. It is not about the old method being better. Best wishes, Norbert ######################################################################## To unsubscribe from the CCP4BB list, click the following link: This message was issued to members o, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity> ________________________________ 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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ________________________________ 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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## 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/
