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<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
