You are right. In this case, I would put some waters in it, refine and see if the density gets any clearer. However, since from this perspective the density is quite far away from the protein, it could be a very disordered PEG, which, even at high resolution, might be impossible to fit.
Best, Herman Von: Abhishek Anan [mailto:rendezvous.a...@gmail.com] Gesendet: Freitag, 3. November 2017 11:10 An: Schreuder, Herman /DE Cc: CCP4BB@jiscmail.ac.uk Betreff: [EXTERNAL] Re: [ccp4bb] another unknown density problem Dear Prof Schreuder Here are another couple of perspectives from coot. The density is too far and isolated from the peptide chain to be an alternate conformation or conformational change. The density of the peptide chain does not look good because it was truncated at 5A for clarity. Best regards Abhishek On Fri, Nov 3, 2017 at 9:33 AM, <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote: Dear Abhishek, To me, it looks like an alternative conformation of the peptide chain or maybe even a conformational change with respect to the starting model. The peptide chain does not look too well defined, despite high resolution electron density. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Abhishek Anan Gesendet: Freitag, 3. November 2017 09:26 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] [ccp4bb] another unknown density problem Hi all, I have an "unknown" density in the map. I have tried to fit it to PEG but it doesn't fit very well. I was wondering if there are other PEG-related or other molecules I could try. The crystal grew in TRIS-HCl and PEG MME 2K. Thank you Abhishek
