Hi Ed, ok, this makes me feel better about this -:) All the best, Pavel On 4/22/13 7:46 AM, Edward A. Berry wrote:
I think this is a good and intuitive way to do it. If you don't do anything, phenix takes care of the interaction as best it knows how. If you define a bond, you are defining the interaction and overriding the automatic definitions. And one thing you can define is to have no interaction within a certain distance range, allowing the xray data to determine the position.
Pavel Afonine wrote:
The only way to turn non-bonded repulsions between two atoms (without involving altlocs) is to define a bond between them, and Nigel's suggestion will let you tune it such that the bond may not actually act as such while disabling non-bonded repulsions. I see it's a bit indirect and rather hackish way of doing this, and it would be way nicer to have a functionality to just say "exclude these atoms from repulsions", but that's not implemented (yet), sorry.
Pavel
On 4/19/13 1:08 PM, Edward A. Berry wrote:
I have a phenix-specific question and a general chemistry question. In a ligand-bound structure, S in an aromatic ring (substituted thiophene) may be H-bonding NH1 of arginine guanidino group. The general question is whether thiophene S can act as H-bond acceptor (assuming one lone pair is in the aromatic pi system for a total of 6 e, the other lone pair is available as H-bond acceptor?).
The phenix-specific question involves whether non-bonded interactions will push the atoms apart during refinement, and how to turn off the nonbonded interaction between these two atoms to allow the xray data to determine the position. Under geometry_restraints.edits I define a bond, but give a very large sigma of 1A. Will this effectively remove non-bonded interactions between these two atoms? _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb