In addition, one should carefully consider the chemistry and coordination geometry around the putative chloride ion. Not only do candidates have to be consistent with the observed omit density, but they must also make chemical interaction and geometry sense. I suspect a partial occupancy water may make the most sense from the limited data provided, but only if all the other placed solvent molecules have clearly defined interactions that do not depend solely on the partially occupied water. What does the chloride coordination geometry look like? Is it clearly a chloride ion and not a cation?
Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Colgate University On Wed, Mar 4, 2020, 12:20 PM 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
