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.
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