-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Kavya,
I assume that you carried out molecular replacement without the ligand in the search model (otherwise you are probably looking at model bias). In that case the ligand most likely has reduced occupancy. You can either manually set all atoms in the ligand to e.g. 0.5 or use the 'occupancy' keyword in refmac to refine it. The density maps should improve. Best, Tim On 05/24/2013 06:50 PM, Kavyashree Manjunath wrote: > Dear users, > > I am using refmac 5.7.0029 for refining a structure (resolution 2.2 > Ang) bound to 2 ligands. After MR There is a very clear density of > ligands but after refinement, I get negative fofc map near one of > the ligand upto 5 sigma. However its 2fofc map covers the whole > ligand. Also for the other ligand, I do not see any 2fofc density > (at 3 sigma) for 2 atoms, without these atoms the ligand is > unrealistic. But the density comes up around these at around 0.7 > sigma. Overall completeness is 99.9% Rmerge 7.5% > > What else I need to check in the data. Kindly provide some > suggestions. > > Thanking you Regards Kavya > > > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRn6QqUxlJ7aRr7hoRAmYhAJ48NmunV8jbKnctniW+06Rn8D/x2QCfd5nR DQHWl1Z5w/XhTsd3RI4+oqQ= =EruH -----END PGP SIGNATURE-----
