On Fri, Jul 23, 2010 at 2:16 PM, Elwood A. Mullins
I'm having issues defining planarity restraints in a .edits file. When all four of the atoms in the plane are selected in a single planarity entry, refinement crashes. When I define a single atom in separate planarity restraint entries (as suggested by Nat), refinement doesn't crash, but the four atoms in the plane are treated as four one-atom planes (obviously useless). My previous correspondence is attached below.
The reason it was crashing is that the atom selection parameter was misnamed, and was being omitted from the final parameters - but since you'd set the sigma, it still tried to create a restraint with an empty selection. After taking another look at the corrected file I sent you, I see I didn't read it closely enough. The atom selection for each plane needs to contain *all* atoms in the plane - unlike the bonds and angles, you do not define individual atoms separately. The correct syntax is actually this: planarity { action = *add delete change atom_selection = "(chain B and resid XX and altid B and (name CD or name CG or name OE1)) or (chain C and resid YY and altid B and name S1P)" sigma = 0.02 } (I've deliberately obfuscated the residue numbers, but you get the idea.) Sorry for the confusion - I was at a conference and attempting to multitask. -Nat