Hello Matthias, Excellent point. Most of the the ordered water are easily visible at 2 rmsd. The central disordered (or partially occupied) water becomes visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have displayed all of the maps). In your opinion, do you think this would be noise?
Jessica On Wed, 4 Mar 2020 at 12:45, Barone, Matthias <bar...@fmp-berlin.de> wrote: > hey Jessica > > a tip that might come up later on anyway: once you put every reasonable > bit into the desity, what I like to to when facing such blobbs: I take a > well defined water out to create a diff density at a position where I know > it is real. Having a feeling of how much you have to contour the diff > density at that point can give you a good feeling how much of noise is > actually in your density right in between the waters..? > > best, matthias > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jessica > Besaw <jbesaw1...@gmail.com> > *Sent:* Wednesday, March 4, 2020 6:42:34 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] A question of density > > Hey Nukri, > > Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure > > I absolutely agree with you on the refinement. I did previously do that, > and I attached the picture. > > What is the BB? > > Cheers! > > Jessica > > > > > > > On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili <sannu...@gmail.com> wrote: > >> Hi Jessica, >> You do not say how well is the rest of the structure refined. >> First, you should refine the structure best you can, without placing >> anything in the unclear blob of your interest so to obtain the best >> possible phases and hopefully improve the blob density as well. >> Then you should let the BB see what that density looks like. Looking at >> only the list of possibilities has very little value without seeing the >> density itself. >> Best wishes, >> Nukri >> >> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw <jbesaw1...@gmail.com> >> wrote: >> >>> Hello friends, >>> >>> I have a "blob" of density in an active site of my protein. >>> >>> I am struggling to determine if I should place a water in this spot, if >>> I should model it as a disordered water, if the density may be a ligand >>> that I have not considered, or if it should be left as unaccounted for >>> density. I would like to publish this structure without compromising the >>> science. >>> >>> I have attached several possibilities that I have considered below. >>> >>> Any suggestions would be appreciated. >>> >>> Cheers! >>> >>> Jessica Besaw >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
