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

[William Scott]

I'd leave it as GDP (or GTP). At least that is what I have done and no one
complained.

Francis E Reyes wrote:
> 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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>>
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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
>
>
>
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