Dear Jon, thanks for your answer. Maybe I have been too quick in writing my last message. The point is that with the old CCP4 interface, I would have been able to run Coot-findwaters to automatically add and remove water molecules at certain DELFWT and FWT rmsd tresholds, respectively, through REFMAC interface. Now, with the new interface, Coot-findwaters is not made explicit anywhere, and DELFWT and FWT rmsd tresholds seem not to be changeable. There’s only "R lower than” that is surely what you say = Rfactor (%) lower than 30%. I would not want to create misunderstandings, I am just asking for things which are not clear to me (maybe given my limited experience), starting from the assumption that my knowledge in refinement, model building and, more in general, protein crystallography, can always improve.
Thanks for the precious help, Luca Mazzei Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy > Il giorno 12 set 2020, alle ore 17:55, Jon Cooper > <jon.b.coo...@protonmail.com> ha scritto: > > Hello, I'm not totally up-to-the minute with this but I didn't know that > refmac itself added waters so maybe it's another program in an i2 pipeline, > or something. However, I know another excellent refinement program that does > ;-) and an excellent graphics program that does, too ;-0 > > In the past, we have added well-defined water molecule when the R-factor goes > into the mid-to-low thirties, or lower. > > Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to > be real but you can lower that cutoff a bit (~1.5) if your resolution is not > brilliant. > > Glad to be corrected on this. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > > > -------- Original Message -------- > On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote: > > Dear CCP4 people, > > I am approaching in these days to the new CCP4i2 interface and, in > particular, to REFMAC. Can anyone quickly explain what the factor R, that > must be chosen in order to automatically add water molecules, is? How can I > relate this value with the previous DELFWT and FWT map values? > > Thanks, > > Luca > > Luca Mazzei - PhD > Department of Pharmacy and Biotechnology > University of Bologna > Viale Giuseppe Fanin, 40 - 40127 > Bologna - Italy > > ######################################################################## > > 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> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > <http://www.jiscmail.ac.uk/CCP4BB>, 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 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/
