[phenixbb] restraints between molecules in adjacent asymmetric units.

Pavel Afonine pafonine at lbl.gov
Thu Dec 4 11:39:02 PST 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-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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://CCI.LBL.gov>
>
> On Thu, Dec 4, 2014 at 9:47 AM, jens j birktoft <birktoft at nyu.edu 
> <mailto:birktoft at nyu.edu>> 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
>     DirectorofCrystallography
>     Structural DNA Nanotechnology
>     Chemistry Department,
>     New York University
>     e-mail: jens.knold at gmail.com <mailto:jens.knold at gmail.com>; Phone:
>     212-749-5057 <tel:212-749-5057>
>     very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
>     +++++++++++++++++++++++++++++++++++++++++++++++++++
>
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