[phenixbb] restrains for nucleaic acid base pairs

Imre Toeroe toro at embl.de
Tue Apr 7 00:22:15 PDT 2009


Dear Pavel,

Thanks for the info. One more question: In half of the DNA the base
pairing is between symmetry related bases as the DNA structure (Holliday
junction) lies on a two-fold axis. Could it be a problem?

Thanks, Imre

Pavel Afonine wrote:
> Hi Imre,
>
> you need to define custom bonds between these pairs:
>
> http://phenix-online.org/documentation/refinement.htm
>
> see section "Definition of custom bonds and angles".
>
> phenix.refine does not do it automatically.
>
> Pavel.
>
>
> On 4/6/09 4:42 AM, Imre Toeroe wrote:
>   
>> Hi,
>>
>> Does anybody know an easy way to restrain nucleic acid base pairs (base
>> stacking+Watson-Crick base pairing) in phenix.refine? I am refining
>> against a 3.3 A dataset.
>>
>> Thanks,
>>
>> Imre
>>
>>
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>>   
>>     
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