While I am sympathetic to Ethan's and George's arguments, what
is missing in the world as it stands is a section in PDB files that
encode the parameters and rules used to generate the riding hydrogen
atoms for that particular model. George has his favorite hydrogen
atoms to build, his favorite bond lengths for placing them (and good
arguments for his selections) and one could, I suppose, look them
up in the documentation for Shelxl, but they should be encoded in
the PDB file to allow automatic regeneration of the hydrogen atoms.

   An explicit listing of the rules for generation is particularly
needed since all these matters can, and often are, modified by the
user. I know that in my refinements I manually move the hydrogen
from one nitrogen to the other in a couple Histidine side chains,
and have created my own rules for hydrogen generation in co-factors.

   CIF tags will have to be agreed upon (and that's always a fun
job) that would allow the description of the details of the various
hydrogen atom generation schemes that are in use, or may be used
in the future. It would also be handy to have a reference implementation,
available under some forgiving license, that would materialize the
hydrogen atoms given the PDB header information, and would reproduce
the exact model refined, for any of the refinement programs.

   This is a worthwhile goal, but a tall order. Until this
infrastructure is in place I think the hydrogen atoms have to be
included in the PDB file. Otherwise it's the same as saying that
I've refined TLS ADP's but not saying what the TLS parameters were
nor listing the atoms in each TLS group.

Dale Tronrud

P.S. George: Do you think hydrogen atoms generated by the "HFIX 137"
command should be deposited? They are placed based on the electron
density map with the dihedral angle of the methyl group becoming a
parameter of the model -- a parameter not recorded anywhere other
than in the hydrogen atom locations.


On 09/14/10 12:41, George M. Sheldrick wrote:
>
> Even though SHELXL refinements often involve resolutions of 1.5A or
> better, I discourage SHELXL users from depositing their hydrogen
> coordinates. There are three reasons:
>
> 1. The C-H, N-H and O-H distances required to give the best fit to
> the electron density are significantly shorter than those required
> for molecular modeling and tests on non-bonded interactions (or
> located by neutron diffraction). It is ESSENTIAL to recalculate
> them hydrogens at longer distances before using MolProbity and other
> validation software.
>
> 2. There is considerable confusion concerning the names to be assigned
> to the hydrogens. This is not made easier by the application of a
> chirality test to -CH2- groups!
>
> 3. O-H hydrogens are particularly difficult to 'see' and the geometrical
> calculation of their positions is often ambiguous. The same applies
> to the protonation states of histidines and carboxylic acids. In
> addition such hydrogen positions are often disordered.
>
> For refinement I recommend including C-H and N-H but not O-H hydrogens.
> For very high resolution structures this reduces Rfree by 0.5-1.0% and
> clearly improves the model. At all resolutions the antibumping
> restraints involving hydrogens are useful.
>
> George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582
>
>
> On Tue, 14 Sep 2010, Dr. Mark Mayer wrote:
>
>> Here's one for the community, which I'll post to both Phenix and CCP4 BBs.
>>
>> Where does the crystallographic community stand on deposition of coordinates
>> with riding hydrogens?
>> Explicit H are required for calculating all atom clash scores with Molprobity,
>> and their use frequently gives better geometry (especially at low resolution).
>> Phenix uses explicit riding H for refinement, and outputs these in the refined
>> PDB. Refmac also uses riding H but does not output H coordinates.
>>
>> While depositing a series of structures refined at 1.4 - 2.75 A with Phenix
>> got the following email from the RCSB, who asked I resupply coordinates
>> without H for two of the structures. Since we can't see H even at 1.4 Å I
>> don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why
>> explicit H atoms used in refinement and geometry validation should be stripped
>> from the file.
>>
>> FROM RCSB
>>
>> We encourage depositors not to use hydrogens in the final PDB file for
>> the low resolution structures (> 1.5 A). Please provide an updated PDB
>> file. We request you to use processed PDB file as a starting point for
>> making any corrections to the coordinates and/or re-refinement.
>> --
>>
>> Mark
>>