[phenixbb] How to keep a custom bond planar ?

[Coincon Mathieu]

Hi,

I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def).
  
      ..-C2-..
          |
-CE-NZ = C1-C3-....


This is a double bond.
Everything work good except for the planarity of the lysine's atoms.


For the bond I wrote in my bond.def:

  bond {
    action = *add
    atom_selection_1 = chain D and resname LIG and name C2
    atom_selection_2 = chain A and resname LYS and resid 66 and name NZ
    distance_ideal = 1.340
    sigma = 0.02
  }

For an angle:

  angle {
    action = *add
    atom_selection_1 = chain D and resname LIG and name C3
    atom_selection_2 = chain D and resname LIG and name C2
    atom_selection_3 = chain A and resname LYS and resid 66 and name NZ
    angle_ideal = 120.000
    sigma = 3
  }

How can I define a plan or some dihedral ??

Or as in the ligand .cif I defined a plan   
 LIG      plan-2    C1        0.020
 LIG      plan-2    C2        0.020
 LIG      plan-2    C3        0.020

 I could add the atoms NZ and CE of the lysine to the plan-2.

Thanks by advance.

And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!)


--------
Mathieu Coicon
PhD Student
Biochimie
Universite de Montreal
(+1)514-343-6111 #5352