Hi, I've generally used PRODRG to create paramater files for any ligands I add during refinement with CCP4 and/or PHENIX. I've been trying READYSET from PHENIX as it greatly helps refining some metal ion positions. But when I use READYSET, any ligand I add (in this case EDO or ethylene glycol) gets modified to contain hydrogens. My resolution is 2.5, definitely not high enough to resolve the hydrogens, so why are they added. Should I just leave them there? I have the same problem with another structure which has bizarre sugar molecules so they are not standard COOT/CCP4/PHENIX small molecules.
As a test, I removed the hydrogens added to the ligands and the refined protein coordinates are way different than when the hydrogens are left in? Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
