What's the resolution? At low res it is possible to miss a subtle movement of e.g. some sidechains which are being replaced by the ligand. What quality parameters did the MR have? Can you omit the entire ligand binding site, refine, and re-generate the map - what does it look like after that?
A picture would help! Artem -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Brenda Patterson Sent: Friday, December 28, 2007 10:56 AM To: [email protected] Subject: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure? Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda
