Dear Dr. Schwieters and other members of Xplor-NIH,
I have been trying the ensemble refinement of a protein‐protein complex with
PRE data using XPLOR-NIH 2.34. I could carry out the ensemble refinement under
standard condition, and now I’m trying the ensemble refinement with one of the
ensemble member held fixed, like Nature (2006) 444, 383 (“The stereospecific
complex was held fixed and other 20 ensembles of non-specific complex were
included in the simulated annealing docking calculations.”), and JACS (2011)
133, 14176 (“ The converged Ne = 1 complex ( obtained from the single ensemble
calculations ) was held fixed and the supplemented Ne = 3 ensembles were
included in the simulated annealing docking calculations. ( Ne = 1 + 3 ensemble
representation) ”).
I tried to fix the coordinates of the ensemble member with memberIndex = 0
during the entire docking protocol by the following description.
_______________________________________________________________________________
dyn_fix = IVM(esim)
dyn_fix.reset()
protocol.torsionTopology(dyn_fix) #manipulator for T-A dynamics
dyn_fix.group( 'resid 301:376' )
dyn_fix.fix( 'resid 6:234' )
dyn_fix.fix( AtomSel('resid 301:376',esim.members(0)) )
_______________________________________________________________________________
However, all ensemble members were held fixed by this description.
I confirmed that the coordinates of all ensemble members except for the member
with memberIndex = 0 were successfully translated by the following script:
_______________________________________________________________________________
from atomSel import AtomSel
from vec3 import Vec3
from atomSelAction import Translate
for i in range(1,esim.size()):
AtomSel("resid 301:376", esim.members(i)).apply(
Translate(Vec3(-0.7,-1.09,-0.445)) )
_______________________________________________________________________________
I guess the selected atoms are stored as the indices of atoms in the groupList,
and the information of simulation gets lost.
I am most grateful if you could tell me how to fix the coordinates of a single
ensemble member while other members are allowed to move freely.
Best Regards,
Hiroki Ogasa,
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