On 23/02/11 16:26, Paul Emsley wrote:
On 23/02/11 16:04, Kendall Nettles wrote:
When I real space refine my the ligand the hydrogens fly away. The ligand
pdb and cif files were generated with PRODRG. I'm using Coot 0.6.2-pre1. Is
this a coot problem, or with the pdb format from PRODRG?
Yes - and no.
Flying hydrogens occur when the PDB atom names do not match the
dictionary names.
I have often seen flying hydrogens. I have never seen flying hydrogens
when the PDB and cif files have been generated with PRODRG (I use the
CCP4 version, just to be clear).
So, at a guess I'd suppose that this is a formatting problem, not a Coot
problem.
OK, so after I bit more investigation, this was more or less the case.
I was a bit shocked to see that the PRODRG web server is still
generating cif restraints that are unconventional/incompatible with the
corresponding PDB file. (I had not looked at this for a couple of years
now.) Given that PRODRG is popular (well, I imagine so), and so are
hydrogens (they should be, at least) and maybe Coot also, I would have
expected to see complaints about this every week! Silent discontents :-(
I use the CCP4 version of prodrg, and that has different hydrogen naming
convention to the web version and the restraints and coordinates _do_
correspond. (The CCP4 version has it's own (different) issues :)
Paul.
