On 17/03/11 14:37, Garib N Murshudov wrote:
First, Coot uses the "old-style" filenames - i.e. the .cif files [1]
are in lettered subdirectories, not all files in one directory
(straightforward for me to fix if you mean to keep the new naming style).
They are not in one directory. The structure is the same as it was
before.
Can you try the version 5.6.25:
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.25.tar.gz
<http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.25.tar.gz>
One version was corrupted. Perhaps you took that version (or I pointed
out to that version)
Ah, that would be it, I guess.
Secondly (and more importantly), the PDB version 3.x has a " H "
hydrogen atom on the peptide N - so did the old-style dictionary.
The new Refmac dictionary does not (it does have HN1 and HN2 -
presumably non-polymer) - hence we still get flying hydrogens -
different ones :-/.
No. It is not. Here is an example (ALA):
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
ALA N N NH1 -0.204
ALA H H HNH1 0.204
ALA CA C CH1 0.058
ALA HA H HCH1 0.046
ALA CB C CH3 -0.120
ALA HB1 H HCH3 0.040
ALA HB2 H HCH3 0.040
ALA HB3 H HCH3 0.040
ALA C C C 0.318
ALA O O O -0.422
That looks better, and not what I was looking at :)
Paul.
