Hi Nika, A couple of other things you could try to improve maps to add to what the others have suggested. One, I am assuming that you are refining the occupancy of the ligand, but if not, that should reduce the negative density? 2. Since you mention soaking the ligand, do you have a good X-ray data set and refined structure of the unliganded protein in the same space group and about the same resolution? If so, you could run an Fo(ligand)-Fo(unliganded) isomorphorous difference map calculation using the phases of the unliganded structure for a map calculation. This may help (or hurt) too.
Best wishes Andy Mesecar On Tue, Nov 24, 2020 at 6:30 AM Nika Žibrat <nika.zib...@ki.si> wrote: > Hello, > > > I have a question about protein-ligand, of which ligand displays an > ambiguous electron density. I am solving a structure of protein with > ligand which was obtained via soaking. Structural characteristics indicate > the ligand is present however the electron density is quite vague and too > small for the size of the whole ligand. I did a Polder map which showed > much larger area of green density. After insertion of my ligand into the > green density in Polder I ran phenix.refine and there is a lot of red on > the spot where the ligand is which was to be expected. This leaves me > wondering how, if even do I incorporate the polder map data into my refine > input. > > > My question is, how do I continue refining and validating the structure in > this case? > > > Thank you, > > > Nika Žibrat > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- *Andrew D. Me**secar* Head, Department of Biochemistry Walther Professor of Cancer Structural Biology Deputy Director, Purdue Center for Cancer Research E-Mail: amese...@purdue.edu _____________________________________________ *Department of Biochemistry Contact Information:* 175 S. University Street W. Lafayette, IN 47907-2063 765-494-1607 ------------------------------------------------------------------ *Research Lab Contact Information:* Hockmeyer Hall of Structural Biology Room 311 240 S. Martin Jischke Drive West Lafayette, IN 47907-1971 765-494-1924 _________________________________________ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
