A few figures in BMC re truncation effects:
http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm Best, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of 00000c2488af9525-dmarc-requ...@jiscmail.ac.uk Sent: Thursday, March 5, 2020 12:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] A question of density 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 <mailto: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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
