Just one correction. NA names are different (instead of * now there are ', as pdb v3.x requires) but values should be same.
Garib
On 17 Mar 2011, at 14:01, Paul Emsley wrote:
> On 17/03/11 12:55, Garib N Murshudov wrote:
>> 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.
>
> Sadly not as easy as that.
>
> 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).
>
> 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 :-/.
>
> So, do I take it that with the new dictionary I now need to apply the mon_lib_list's data_mod_list items for the peptides (in this case DEL-NH1 and DEL-OXT) when Coot finds a peptide link? It seems to me that if this dictionary is out in the wild I'll need to sort this out pretty sharpish.
>
> Paul.
>
> [1] the Corina manual calls CIF files "CCP4 dictionary files" :-)
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