[phenixbb] Making GDP (non-polymer) into an RNA monomer

[Francis E Reyes]

Thanks for the quick reply and working solution!

However, what's the etiquette for how the residue should be named in  
the PDB? I have it right now as GDP, though Gr seems much more  
sensible? Or should I name it something completely custom?

Thanks

FR

On Feb 8, 2008, at 2:20 PM, William Scott wrote:

> I've done just that with GTP, so with minor changes, this should work:
>
>  geometry_restraints.edits {
>    bond {
>      action = *add delete change
>      atom_selection_1 = "chain A and resid 1 and name O3\\*"
>      atom_selection_2 = "chain A and resid 2 and name P"
>      symmetry_operation = None
>      distance_ideal = 1.59
>      sigma = 0.01
>    }
>    angle {
>      action = *add delete change
>      atom_selection_1 = "chain A and resid 1 and name C3\\*"
>      atom_selection_2 = "chain A and resid 1 and name O3\\*"
>      atom_selection_3 = "chain A and resid 2 and name P"
>      angle_ideal = 120
>      sigma = 1
>    }
>  }
>
>
> Francis E Reyes wrote:
>> All
>>
>> I need to attach a 5' modification, a diphosphate guanosine to my  
>> RNA.
>> I figure GDP (from the monomer library) has everything I need.
>> However, what needs to be done to make a connection with the next
>> nucleotide in the chain (in both phenix.refine and coot) ?
>>
>> Thanks
>>
>> FR
>>
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
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>>
>>
>>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D