[ccp4bb] how to refine RNA with two phosphate at 5' by phenix

[Lisa Wang]

hi all,
I have one structure contains dsRNA with two phosphate group at 5'.. I named
the first residue GDP and got a cif file by running phenix.elbow. Then I
refine my structure by running phenix.refine my.pdb my.cif. But the fist and
the second residue do not link with each other, that is no bond between O3*
of the fist residue and P of the second residue.
Please give me some idea. Thanks

Re: [ccp4bb] how to refine RNA with two phosphate at 5' by phenix

[Ralf W. Grosse-Kunstleve]

In the most recent phenix.refine version, the links should be automatic if the
backbone atom names are consistent with the naming for standard RNA residues.
Let me know if you're having problems with phenix 1.6 or 1.6.1.
Ralf



- Original Message 
From: William G. Scott wgsc...@chemistry.ucsc.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, April 2, 2010 5:07:09 PM
Subject: Re: [ccp4bb] how to refine RNA with two phosphate at 5' by phenix

Lisa Wang wrote:
 hi all,
 I have one structure contains dsRNA with two phosphate group at 5'.. I
 named
 the first residue GDP and got a cif file by running phenix.elbow. Then I
 refine my structure by running phenix.refine my.pdb my.cif. But the fist
 and
 the second residue do not link with each other, that is no bond between
 O3*
 of the fist residue and P of the second residue.
 Please give me some idea. Thanks


You have to explicitly link them.  Something like the following:

  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
}
  }