[phenixbb] Phenix.refine Restraints: replicating refmac external restaints
elliot.nelson at dtc.ox.ac.uk
Thu Jan 19 00:49:37 PST 2017
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
with the bold residues restrained to one another. Hope this makes sense.
From: Pavel Afonine [pafonine at lbl.gov]
Sent: 18 January 2017 18:28
To: Elliot Nelson; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Phenix.refine Restraints: replicating refmac external restaints
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:
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.
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?
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