Thanks Pavel, that works well. Best, -Andy On 9/29/2009 12:21 PM, Pavel Afonine wrote:
Alternatively, you can do simply this:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain F and resid 1 and name FE1 atom_selection_2 = chain A and resid 69 and name SG distance_ideal = 2.35 sigma = 0.1 slack = None } }
Pavel.
On 9/29/09 8:54 AM, Andrew T. Torelli wrote:
Hi all,
I'm having what I believe is a simple problem defining custom bond restraints between a side chain in my protein model and a ligand (non-covalent bond). Here is a minimal form of my custom bond definition file that suffers from the error:
refinement.geometry_restraints.edits { Atom1 = chain F and resid 1 and name FE1 Atom2 = chain A and resid 69 and name SG bond { action = *add atom_selection_1 = Atom1 atom_selection_2 = Atom2 distance_ideal = 2.35 sigma = 0.1 slack = None } }
I'm using phenix 1.4-153 and I get the following error: ERROR: Unused parameter definitions: refinement.geometry_restraints.edits.Atom1 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) refinement.geometry_restraints.edits.Atom2 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
I've checked through the online manual and I believe my syntax is correct, but I'm not sure why my custom bond restraint is being ignored.
A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs?
Thank you very much for your help, -Andy
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