[phenixbb] phenix.ready_set hydrogens not compatable with coot library

[Jeff Headd]

> I guess (not entirely sure) that if you use a recent Coot version then you
> shouldn't have problems with hydrogens. At least they don't fly away at the
> first touch. I just tried myself.

There are still some hydrogen atoms that will fly off into space in
Coot.  The naming changes in proteins that seem most effected are
those atom sets where the numbering changed, such as HB1 and HB2 in
PDB version 2.3 to HB2 and HB3 in PDB version 3.x.  DNA hydrogens also
will fly off into space, as can some ligands.

> Actually, phenix.reduce can output v2 formatted PDB. I guess it is "-OLDpdb"
> keyword. So if you really like to stick to the older format you can.

This option doesn't entirely solve the problem because it doesn't
change the heavy atom naming conventions.  Not a huge deal in
proteins, but a bigger problem in RNA/DNA.  When using the "-OLD" flag
in Reduce it is expecting that the heavy atoms conform to PDB 2.3, so
the hydrogen atoms won't be added correctly if you mix and match nor
will any changes to the heavy atoms be made.

Jeff