Just for info:
There is new version of the dictionary that is compliant with pdb v3.
It works with new version of refmac and should work with phenix also.
It seemed to work with coot also.
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/remfac_dictionary_v5.18.tar.gz
I should warn that we are still working on this dictionary but it
should be usable now (if you use refmac then you will need newer
version of refmac also available from the same page)
regards
Garib
On 16 Mar 2010, at 19:56, Paul Emsley wrote:
> Martin P. Horvath wrote:
>> I am refining with 1.14 Å data and have included riding hydrogen
>> atoms. In
>> addition to (and perhaps related to) certain difficulties with real-
>> space
>> refinement caused by nomenclature mismatch phenix/coot, the alpha-
>> carbon
>> hydrogen is not removed when deleting an alternate conformation
>> residue. For
>> each residue previously with two alternate conformations, reduced
>> to one
>> conformation, the H atom retains A and B tags with partial
>> occupancy. This
>> is easy to clean up with a text editor, or by running phenix.reduce
>> -trim;
>> phenix.ready_set, however, if there are plans to smooth out model
>> building
>> with hydrogens...
>>
>
> OK, I should fix that right away.
>
> As an aside, re: the dictionary in general:
>
> Coot is distributed with a copy of the refmac library, which has PDB
> version 2.3 atom names.
>
> You can override that dictionary by setting up CCP4 in the normal way.
> You can further override the dictionary by setting the environment
> variable COOT_REFMAC_LIB_DIR
>
> So if Phenix distributes a version of the monomer library that has
> PDB version 3.x atom names then Coot can use that if you point to it.
>
> Paul.
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