Dear Nika, A tool I am gaining experience with, but for a challenge like you describe, may help:- In Coot>Calculate you see “Blurring/Sharpening tool”. You are presented with a choice of electron density map (here you would select your Fo-Fc). There is then a slider tool, to the left and to the right, and you can see the impact of negative or positive B factor on your map. Blurring, slide right, may assist your density continuity versus Sharpening, slide left, which may assist the detail of your map. The logic of the tool is that your diffraction data, and of the Fo-Fc differences, can be fine tuned, in or out. Best wishes, John
Emeritus Professor John R Helliwell DSc > On 24 Nov 2020, at 11:29, 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 ######################################################################## 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/
