Re: [phenixbb] restraints between molecules in adjacent asymmetric units.

4 Dec 2014

      Hi,

I would like to see this example too.

You can define a bond between any pair of atoms, any number of bonds, 
including bonds between symmetry related atoms. This is explained in 
details here:

http://phenix-online.org/documentation/reference/refinement.html#definition-...

Example:

refinement.geometry_restraints.edits {
   bond {
     action = *add
     atom_selection_1 = chain A and resseq 123 and name O
     atom_selection_2 = chain Z and resseq 321 and name N
     symmetry_operation = -x-1/2,y-1/2,-z+1/2
     distance_ideal = 1.55
     sigma = 0.02
   }
}

The best way to check that the bond you defined was actually used in 
refinement is to find it in .geo file that lists all restrains used in 
refinement.

Pavel

On 12/4/14 10:47 AM, Nigel Moriarty wrote:
...
Jens
You should try
phenix.ligand_linking model.pdb
to see if that is helpful. I think, though, that you should send me an 
example so I can check the best method.
Cheers
Nigel
---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : [email protected]
Fax   : 510-486-5909       Web  : CCI.LBL.gov http://CCI.LBL.gov
On Thu, Dec 4, 2014 at 9:47 AM, jens j birktoft mailto:[email protected]> wrote:
Hi Everybody.
Are there ways to restrain non-covalent interactions between
    molecules in adjacent asymmetric units?
    I know the custom bond procedure works well for covalent bonds.
    However I also would like to add restraints for (1) bond angles,
    (2) torsion angles (less important) and (3) nucleotide
    base-pairing. I know that all of these can be generated via the
    custom bond syntax, but that is a rather tedious and
    time-consuming process.  Perhaps there is a simpler way
I know this issue has been raised before but am unaware of any new
    developments.
Cheers
Jens
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    +++++++++++++++++++++++++++++++++++++++++++++++++++
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    DirectorofCrystallography
    Structural DNA Nanotechnology
    Chemistry Department,
    New York University
    e-mail: [email protected] mailto:[email protected]; Phone:
    212-749-5057 tel:212-749-5057
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Re: [phenixbb] restraints between molecules in adjacent asymmetric units.

Pavel Afonine