Series termination is a problem when you leave out Fourier coefficients that have significant amplitude. Back in the old days when we cut data aggressively it was something to worry about. Now that most everyone integrates down to very weak intensities it shouldn't be much of a problem.
Besides, as Glusker and Tureblood noted, a peak in a difference map (the green blob in this discussion) cannot be caused by series termination. If there is series termination the shape of a difference map peak can be affected, but not the presence of the peak itself. Dale Tronrud On 3/5/2020 12:20 PM, 00000c2488af9525-dmarc-requ...@jiscmail.ac.uk wrote: > Hello, not sure if anyone has mentioned series termination errors in the > vicinity of electron dense atoms. The attached is from Glusker & > Trueblood and might be of interest. > > Jon Cooper > > On 5 Mar 2020 19:00, Jessica Besaw <jbesaw1...@gmail.com> wrote: > > 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 > <mailto: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 > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jessica Besaw > <jbesaw1...@gmail.com <mailto:jbesaw1...@gmail.com>> > *Sent:* Wednesday, March 4, 2020 6:42:34 PM > *To:* CCP4BB@JISCMAIL.AC.UK <mailto: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 <mailto: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 <mailto: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 > > > > ------------------------------------------------------------------------ > > 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
