In reasonably compact format, the discussion topic is summarized in this CCP4 weekend introduction
https://journals.iucr.org/d/issues/2013/02/00/wd5191/index.html As far as the solvent exclusion self-deception via low occupancy goes, fig 2 here: https://febs.onlinelibrary.wiley.com/doi/epdf/10.1111/febs.14320 Good luck, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Nika Žibrat Sent: Tuesday, November 24, 2020 03:29 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] phenix.refine with ligand with ambiguous electron density 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 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &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/
