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-of-custom-bonds-and-angles

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

On Thu, Dec 4, 2014 at 9:47 AM, jens j birktoft <[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

--

+++++++++++++++++++++++++++++++++++++++++++++++++++
Jens J. Birktoft

Director of Crystallography

Structural DNA Nanotechnology

Chemistry Department,
New York University

e-mail: jens.knold@gmail.com; Phone: 212-749-5057
very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
+++++++++++++++++++++++++++++++++++++++++++++++++++

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