Making GDP (non-polymer) into an RNA monomer
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 gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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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
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- 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
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
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- 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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Francis E Reyes -
William Scott