Dear Fellows of the Bond,
when validating a QM refined homology model with Molprobity, I noticed various 8 sigma deviations in the carbon-hydrogen bond distances. Out of curiosity, I then used refmac to calculate riding Hs for the same model, and at least in one instance (N-H backbone) there are significant differences between Molprobity and Refmac H bond distances (differences to the QM distances in other instances I find interesting, but less relevant for us). The riding H vs Molprobity presumably should be consistent, because if we use them in VDW restraints but they differ from the validation target, systematic bias will occur. I have no feel how significant that effect might be - maybe someone more erudite can comment. Examples distance MP REF QM backbone N-H 0.86 1.01 1.00 phenyl C-H 0.93 0.93 1.09 Best, BR PS: If someone has accurate experimental values for CH distances I'd appreciate a link. No access to CSD. ------------------------------------------------------ Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:[email protected]> [email protected] +1 925 209 7429 +43 767 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------
