At least last fall, the state of the art for getting your T7-transcribed RNA to
start with a triphosphate in phenix was to add this file (edited for your
chains, of course) through the gui (if you use the gui).
Thanks to Deepak Koirala and Nigel Moriarty for help in working this out.
* Phoebe
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = chain A and resname GTP and name O3'
atom_selection_2 = chain A and resid 594 and name P
symmetry_operation = None
distance_ideal = 1.6
sigma = 0.02
slack = None
}
angle {
action = *add
atom_selection_1 = chain A and resname GTP and name C3'
atom_selection_2 = chain A and resname GTP and name O3'
atom_selection_3 = chain A and resid 594 and name P
angle_ideal = 120
sigma = 1
}
bond {
action = *add
atom_selection_1 = chain B and resname GTP and name O3'
atom_selection_2 = chain B and resid 594 and name P
symmetry_operation = None
distance_ideal = 1.6
sigma = 0.02
slack = None
}
angle {
action = *add
atom_selection_1 = chain B and resname GTP and name C3'
atom_selection_2 = chain B and resname GTP and name O3'
atom_selection_3 = chain B and resid 594 and name P
angle_ideal = 120
sigma = 1
}
}
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Almudena Ponce
Salvatierra <maps.fa...@gmail.com>
Reply-To: Almudena Ponce Salvatierra <maps.fa...@gmail.com>
Date: Friday, April 12, 2019 at 10:43 AM
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] naive question how to add GTP as a residue to a nucleic acid
chain and refine!
Dear all,
I would like to add a GTP residue to a nucleic acid chain. For so I followed
the following steps in coot: add monomer from library, GTP, changed chain ID
and residue number accordingly, and then Extensions --> Modelling --> link 2
atoms. I got a dashed line between the 3'O of the GTP and the phosphate of the
neighboring nucleotide, and then I used the real space refine tool. Up to here,
it all looked promising.
In phenix refine I run elbow and readyset and provided cif files, but after
phenix.refine I find out that the link between GTP and it's neighbor is gone.
How to preserve the bond?
Thank you very much in advance!!
Best,
Almudena
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