Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). Best Leonid JEROME JOHNSON wrote:
Hello all,
I'm happy to join the forum! I have a problem with clashscores and would be grateful for support.
I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30.
I wondered if you could describe the best way to reduce these?
Attached is my latest round of refinement should you wish to take a look!
Best, Jerome