selectively remove bond length restraints on atoms
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hello, What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file: refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } } but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } } is it a good way to deal with the problem ? thanks in advance for your help. Maxime
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Sorry this isn't supported right now. I'm currently working on the
restraints system, so there is hope that it will work eventually.
Ralf
On Thu, Mar 15, 2012 at 8:20 AM, Maxime Cuypers
hello,
What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file:
refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } }
but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands
refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } }
is it a good way to deal with the problem ? thanks in advance for your help.
Maxime
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On Thu, Mar 15, 2012 at 8:20 AM, Maxime Cuypers
What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine?
This isn't a perfect solution, but I recently added an option to change the weight on selected geometry restraints: refinement.geometry_restraints.edits { scale_restraints { atom_selection = chain A and resseq 1000 and name MG scale = 0.0 apply_to = *bond } } The intended purpose was actually to increase the geometry weight on problematic regions of the structure, but the reverse should be possible. Note however that this will effectively cancel out *all* bond restraints for the selection, not a specific linkage. -Nat
participants (3)
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Maxime Cuypers
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Nathaniel Echols
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Ralf Grosse-Kunstleve