Hi Phoebe,
that actually worked! thank you very much!
Best,
Almudena
El mar., 16 abr. 2019 a las 20:32, Phoebe A. Rice (<pr...@uchicago.edu>)
escribió:
> 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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