View source for RDC Refinement with XPLOR-NIH

===== Brief Description  =====

Residual Dipolar Couplings (RDCs) originate from the anisotropic component of the dipolar interaction, which is dependent on the angle between an inter-nuclear vector and the magnetic field. When a molecule samples orientations uniformly, as it does in normal solution NMR, dipolar couplings average to zero and are not observable. However, if a molecule is dissolved in a dilute liquid crystalline medium, or other orienting medium, it becomes partially aligned, and the dipolar couplings are not completely averaged to zero.&nbsp; This leads to a small contribution to the splitting of NMR signals. The angular dependence of these contributions can provide valuable structural information that complements NOE distance restraints.&nbsp; RDCs can be used to validate protein structures, to refine structures to improve quality, and to provide constraints as a part of an initial structure determination. Here, we describe the RDC-refinement protocol using XPLOR-NIH. The python version of the refinement script was taken from the example dataset (xplor-nih-2.22/eginput/gb1_rdc/refine.py) provided by the XPLOR-NIH package. The key features of this refinement are as follow: 
<div></div> 
:- Variable tensor tools for floating the RDC tensors during refinement 
:- A radius of gyration term to represent the weak packing potential 
::(This potential is used when the calculated structures are too loosely packed) 
:- Database potentials of mean force to refine against: 
::- Multidimensional torsion angles 
::- Backbone hydrogen bonding database (Optional)

<br> 

===== Software Information  =====

XPLOR-NIH <br> http://nmr.cit.nih.gov/xplor-nih/ <br> <br> REDCAT <br> http://ifestos.cse.sc.edu/software.php <br> 

===== Files Need to Run XPLOR-NIH  =====

The following files in XPLOR format are required to run the refinement: 

:'''prot_noe.tbl''' NOE restraint table (converted from CYANA upl file using a CYANA to XPLOR conversion script) 
:'''prot_dihe.tbl''' Dihedral angle restraint (Use CYANA for format conversion) 
:'''prot_rdc.tbl''' RDC restraint table 
:'''prot.psf''' and '''prot.pdb''' Startup psf and pdb files were generated using the lowest energy structure from CYANA.

===== Protocol for RDC Refinement  =====

First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either REDCAT or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program. 
<pre>#                        medium  Da   rhombicity
for (medium,Da,Rh) in [ ('t',   -6.5, 0.62),
                        ('b',   -9.9, 0.23) ]:
    oTensor = create_VarTensor(medium)
    oTensor.setDa(Da)
    oTensor.setRh(Rh)
    media[medium] = oTensor
    pass
</pre> 
<br> The example below contains NH, NCO, and HNC RDCs from two different alignment media. The Da rescaling factor was used since the magnitude of the non-NH RDCs were not normalized to the magnitude of NH RDCs. 
<pre>from rdcPotTools import create_RDCPot, scale_toNH
rdcs = PotList('rdc')
for (medium,expt,file,                 scale) in \
    [('t','NH' ,'tmv107_nh.tbl'       ,1),
     ('t','NCO','tmv107_nc.tbl'       ,.05),
     ('t','HNC','tmv107_hnc.tbl'      ,.108),
     ('b','NH' ,'bicelles_new_nh.tbl' ,1),
     ('b','NCO','bicelles_new_nc.tbl' ,.05),
     ('b','HNC','bicelles_new_hnc.tbl',.108)
     ]:
    rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])

    #1) scale prefactor relative to NH
    #   see python/rdcPotTools.py for exact calculation
    # scale_toNH(rdc) - not needed for these datasets -
    #                        but non-NH reported rmsd values will be wrong.

    #3) Da rescaling factor (separate multiplicative factor)
    # scale *= ( 1. / rdc.oTensor.Da(0) )**2
    rdc.setScale(scale)
    rdc.setShowAllRestraints(1) #all restraints are printed during analysis
    rdc.setThreshold(1.5)       # in Hz
    rdcs.append(rdc)
    pass
potList.append(rdcs)
rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") )
</pre> 
<br> Allow Da and R to float by using the setFreedom method associated with the medium object. To fix the peptide plane, the IVM_groupRigidBackbone tool were used (First two lines and the last line). 
<pre>from selectTools import IVM_groupRigidBackbone
IVM_groupRigidBackbone(dyn)

for m in media.values():
#    m.setFreedom("fixDa, fixRh")        #fix tensor Rh, Da, vary orientation
    m.setFreedom("varyDa, varyRh")      #vary tensor Rh, Da, vary orientation
protocol.torsionTopology(dyn,oTensors=media.values())

# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
IVM_groupRigidBackbone(minc)
</pre>