> > Riding hydrogens are *not* part of your model, > > The fact that you don't see H in your fo-fc map due to limited > resolution and high level of noise does not mean that H atoms are not > present in actual real structure -:) >
Let me ask you this - are bond length restraints part of the *model*? Obviously not, they are part of refinement target. In the same way riding hydrogens are used to calculate the refinement target, but they do not increase the number of parameters of your model. So I guess my definition of the "model" excludes deduced parameters. > Not all programs and their versions place H atoms the exact same way > (using same geometry values, same rules for B-factors assignment: in > some programs H inherit the B-factors of the atom it's attached to, in > some it is multiplied by the factor from 1.1... to 1.5, etc. What > about occupancies, especially for alternate conformations?). But as I said, (if) the program and version is included in the PDB file, riding hydrogens can always be reconstructed. > Again, it's matter of just one command to remove H atoms from your PDB > file, but it's not so straightforward to add them back the exact same > way they were before. So, its much easier to keep them, rather then > spend time on finding the good reasons for removing -;) What's easy is not always right :) -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
