Phenix.refine Restraints: replicating refmac external restaints
Hi All, Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e: Equivalent of: exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1 would be : refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } } If this is incorrect: Am i missing another way to create external restraint functionality in phenix, or am I making a more fundamental misunderstanding of how restraints are handled in both programs? Thanks in advance Elliot Nelson
Hi Elliot,
Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e:
Equivalent of:
exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1
would be :
I don't know how restraints function in Refmac.
refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } }
This will define a bond between these two atoms by adding a term to the restraints: (1/sigma**2)*(distance_model - distance_ideal)**2 Note, you can add as many of such bonds as you with. Also, using similar syntax you can add angles, planes, torsions, etc. Just out curiosity and if it's not a secret: what are you trying to achieve? Pavel
Hi Pavel, I'm aiming to restrain residues adjacent to alternate conformers, such that the alternate conformers are not able to significantly drift from initial positions within the refinement cycle. i.e Residue with two alternate conformers/altlocs A and B All-All-A/B-All-All becomes All-A-A-A-All All-B-B-B-All with the bold residues restrained to one another. Hope this makes sense. Thanks Elliot ________________________________ From: Pavel Afonine [[email protected]] Sent: 18 January 2017 18:28 To: Elliot Nelson; [email protected] Subject: Re: [phenixbb] Phenix.refine Restraints: replicating refmac external restaints Hi Elliot, Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e: Equivalent of: exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1 would be : I don't know how restraints function in Refmac. refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } } This will define a bond between these two atoms by adding a term to the restraints: (1/sigma**2)*(distance_model - distance_ideal)**2 Note, you can add as many of such bonds as you with. Also, using similar syntax you can add angles, planes, torsions, etc. Just out curiosity and if it's not a secret: what are you trying to achieve? Pavel
participants (2)
-
Elliot Nelson -
Pavel Afonine