On 12/18/2008 7:23 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 -:)
There are definitely some (many) parameters that are never included in
the deposited pdb file.
This is true. However, whatever affects the R-factor values has to be
included (there are not that many parameters). Same for geometry.
Some are built into software, some simply
omitted.
It's ok if they are omitted BEFORE R-factors and geometry statistics
calculation, otherwise it's not good.
This may be wrong, but in my humble opinion riding hydrogens
are easy to recalculate and thus their inclusion constitutes redundancy.
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?).
BTW, I've seen some deposited pdb files which had water molecules given
with hydrogens (e.g. 1aa7 - 2.1A resolution, and look - hydrogens have
zero (!) B-factors).
There are many strange files there, even after remediation. Here is
another one:
http://www.rcsb.org/pdb/files/2atb.pdb
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 -;)
Cheers,
Pavel.
