Sara Zueger wrote:
Hi everybody,
Hi Sara,
as I did not find a final solution to the hydrogen restraints problem
(flying or exploding during real space refinement) in any of the mailing
lists, I wanted to pick this topic up again.
If one adds hydrogens by phenix.ready_set or reduce the labels for these
hydrogens on let's say a Cbeta atom will be HB2 and HB3 (according to the
pdb v3.2 convention). However, the coot/ccp4 library names them HB1 and HB2,
so there are no restraints for HB3 atoms. I see that probably this naming
problem can be overcome by using phenix.reduce -OLD, or renaming them
manually in the pdb file (but if one deposits the structure to PDB does one
have to name them back again?). Is there already some new solution?
There is not a solution yet.
And how about hydrogen restraints for the most N-terminal amino acid, where
one has H1, H2 and H3? How are these handled? There seem to be no restraints
for those as well, because they also fly around during real space refinement.
Same situation.
We need to do some drudge work to convert the hydrogen names in the
libraries. AFAICS it is straightforward, but just hasn't been done by
anyone in the CCP4/Coot community.
I wonder what dictionary the Phenix fellow use? If they have updated
the dictionary to 3.2 format, perhaps we could use their copy too.
(However, we deal with this, it should be done by the end of the 0.7.x
series.)
Paul.
