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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