Upgrading dictionary should be just matter of downloading from this site:
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.6.0023.tar.gz
or from the latest ccp4 (6.1.24 or something like that)
Garib
On 17 Mar 2011, at 12:54, Paul Emsley wrote:
> On 16/03/11 18:45, Dr. Mark Mayer wrote:
>> Dear all,
>>
>> I'm rebuilding structure refined using phenix -1.7-650 using coot
>> 0.6.2-pre-1-250.
>> When I use the rotamers command to select new rotamers (flagged as
>> bad by molprobity) some of the riding H atoms get left behind, which
>> means the file is no good for further crystallographic refinement.
>> Likewise, real space refinement produces the infamous flying hydrogens problem.
>>
>> Any ideas on fixing this? Our current work around is to remove H and
>> then run reduce again prior to refinement in phenix.
>>
>>
>
>
> This is not a Coot problem. There is a mismatch between the model and the dictionary (presumably version 3.x and 2.3).
>
> The dictionary needs to be upgraded to 3.x - it is not hard work but needs to be done. I have scheduled it for 0.7 if it is not done before I do it - for standard protein residues, RNA and DNA at least.
>
> You are using the approved work-around.
>
> Paul.
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