[phenixbb] ligands at a special position

[Subhani Bandara]

Hi Ralf,

Thanks a lot for the fast response.
I have actually tried setting all occupancies to 0.5 and it didn't work.
Also I could find how to define custom bonds, but I am not clear with how to
use symmetry operations and pseudo bonds (I know how to turn on symmetry in
coot). Following are the commands I came up with for custom bonds

refinement.geometry_restraints.edits {

bond {

action  = *add

atom_selection_1 = chain y and resseq 2 and name N1

atom_selection_2 = chain y and resseq 2 and name C4

distance_ideal = 3.0

sigma = 0.02

slack = None

}

bond {

action  = *add

atom_selection_1 = chain y and resseq 2 and name N1

atom_selection_2 = chain Z and resseq 1 and name TB

distance_ideal = 2.5

sigma = 0.02

slack = None

}

}
Also if I want to run refine in GUI can I give these commands as an input
file? If so what is the file format I should use?

Thanks in advance
Subhani

On Mon, Oct 17, 2011 at 2:50 PM, Ralf Grosse-Kunstleve <
rwgrosse-kunstleve at lbl.gov> wrote:

> So I left only half of that DPA ligand structure on PDB file and changed
>> the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other
>> atoms of the half ligand structure at 1.00.
>>
>
> Keep the occupancy of N1 and C4 as 1.00, then phenix.refine should
> automatically detect those as special positions and keep them exactly on the
> two-fold axis.
> The bonds and other restraints to the atoms on special positions will not
> work automatically. Currently, the only option is to define custom bonds
> (see phenix.refine docs) with symmetry_operation=x,y,z. You can use Coot to
> obtain the symmetry operation (turn on drawing of symmetry copies; when
> clicking atom Coot will show the sym op). Emulate angle and dihedral
> restraints with pseudo-bonds. Inspect the .geo file to verify that all
> restraints are correct.
>
> You can also keep all DPA atoms, with all occupancies set to 0.5. Then the
> restraints will work as usual; probably you don't have to do anything
> special. However, the N1 and C4 are allowed to float around the special
> position. It may be OK though. I think I'd try this option first.
>
> Ralf
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111019/b010fd10/attachment.htm>