Hi Bill,
Sorry if my first message was confusing. I do want to convert from A
to 2AP.
I'm working on following Paul Emsley's suggestions.
Thanks! and all the best,
--Buz
On Mar 28, 2009, at 11:48 AM, William Scott wrote:
> On Sat, March 28, 2009 5:37 am, Paul Emsley wrote:
>> Buz Barstow wrote:
>>> Dear All,
>>>
>>> I'd like to add substitute a natural base (adenine) for a non-
>>> natural
>>> base (2-aminopurine), in a molecular model of an RNA molecule.
>>>
>>> I'd like to do this with CCP4 and Coot. Could I ask for some help
>>> please?
>>
>>
>> The "CCP4 way" would be to use sketcher and search for aminopurines.
>> You will find 2,6-diaminopurine (1AP). Load this up and delete the
>> 6-amino group to convert to 2-aminopurine. Save the coordinates and
>> dictionary (give it a new name).
>>
>> Fire up coot and File -> Import CIF dictionary...
>>
>> Centre on the residue you want to substitute
>>
>> Extensions -> Modelling -> Replace residue -> 1AP (or whatever you
>> called it).
>>
>> (If you have a map loaded when you do this, it will try to fit to
>> that
>> as a final step)
>>
>> Paul.
>>
>
> I may be mistaken, but I thought he was asking how to mutate from
> 2AP to
> A. (If you use simple mutate, you get a menu of 20 amino acids to
> choose
> from.)
>
> Bill
>
>
>
> William G. Scott
>
> Contact info:
> http://chemistry.ucsc.edu/~wgscott/
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