On 12/18/2008 8:23 AM, Ed Pozharski wrote:
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.
- "bond length restraints" do not contribute to the scattering and hence
do not affect the R-factors, while H atoms do contribute to scattering
and therefore R-factors computed from the model with or without
hydrogens can be different (I spent a couple of months implementing it
in PHENIX and I can say for sure that the difference is well noticeable).
- the (slightly) different geometry library values for hydrogens will
obviously lead to different positions for H atoms which has a great
potential to yield different validation results (for example, clash
scores in Molprobity).
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.
What about 50 years from now? Are you sure you will be able to dig out
that xxx.zzz.aaa version of that program, install it and run? I would
assume it will be much easier to take a complete model from data base.
Pavel.
