Hi Nika, Here you need some common sense. The green density in you polder map may just be the bulk solvent that was removed from the model to generate the polder map. In this case you have to use common sense and ask yourself a couple of questions:
* Is the density really from the ligand, of from some other component from your crystallization solution? Molecules like tris or hepes love it to masquerade for ligands of interest. * Could it be that only part of the ligand is visible because the other parts are disordered or not present? This happens quite often. Instead of the full-ligand, a break-down product or reaction intermediate might have bound, or part of the ligand binding site is occupied by crystal contact. In this case I would fit the part of the ligand which has convincing electron density, refine and look at the electron density maps to see if the fit to the density is convincing and if additional atoms could be added to the ligand. If you cannot fit the whole ligand, even after some efforts, I would submit a partially fitted model. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Nika Žibrat Gesendet: Dienstag, 24. November 2020 12:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: [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&A=1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C56080723579a4530a08008d8906c42c0%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637418142105522594%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=pebjZIXHZMUjaHn7qx55Io7vA%2F2TmW4h4Sgeio38wCs%3D&reserved=0> ######################################################################## 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/
