Session 5

1. Resonance to atom link

An Nmr.Resonance describes the NMR signal arising from an atom (or
group of atoms). In contrast to the 'classical' meaning of an NMR
resonance, this CCPN object relates to a 'generic' signal that is not
specific to a set of conditions or field strengths.  

The Nmr.Resonance connects all NMR information together, so that, for
example, you can define that this particular shift value and this peak
assignment are both attributable to a particular Nmr.Resonance.  

Nmr.Resonances can be 'assigned' by connecting them to MolSystem.Atoms
via Nmr.ResonanceSet and Nmr.AtomSet objects (see
http://www.ebi.ac.uk/msd-srv/docs/NMR/NMRtoolkit/linkResonances.html
for a figure and some example linking schemas). This link describes
the ambiguity of the assignment, so that it is clear whether
Nmr.Resonances linked to prochiral atoms are stereospecifically
assigned (or not). Finally, when changing an assignment for an
Nmr.Resonance, all related NMR information is instantly linked to the
correct Atoms (i.e. the assignment only has to be modified in one
single place).  

Exercise 1.1:

  1. Create protein chain with residues WHATSTHISCCPNAPILIKE
  
  2. Connect Nmr.Resonance(s) in the correct way to the following
       atom(s):
  
     - Ile 16 HB
     - Trp 1  CZ3
     - Ser 5  HB2 and HB3 stereo assigned
     - Ser 9  HB2 and HB3 ambiguous
    
     Also print out the information contained in the Nmr.Resonance ->
       MolSystem.Atom linkage.

     Hint: in each case:

     1. Find the correct residue and atom.
     2. Make new resonance(s) with the right isotope types.
     3. Make new atomSet(s) from the atom information.
     4. Connect the right atomSets to the right resonances using
          resonanceSet object(s).


 Exercise 1.2:

  1. Create protein chain with residues WHATSTHISCCPNAPILIKE
  
  2. Using similar methods as in exercise 1.1 and the help given below, 
       connect Nmr.Resonance(s) in the correct way to the following
       atom(s):
  
     - Ala 3  HB*
     - Leu 17 HD1* and HD2* ambiguous
    
     Note that you have to create Nmr.AtomSet(s) linked to all three
       MolSystem.Atoms in the methyl group. The best way to do this is to go
       via the ChemComp reference information to get the ChemAtomSet(s)
       describing the methyl group, then find the correct MolSystem level
       atoms based on this data.

     Also print out the information contained in the Nmr.Resonance ->
       MolSystem.Atom linkage.


2. Nmr measurements

NMR measurements are all directly linked to one or more resonances.

Exercise 2.1:

  1. Create 10 new Nmr.Resonances (they don't have to be linked to
       atoms!).
  
  2. Create an Nmr.ShiftList and create 10 Nmr.Shifts, each linked to
       a different resonance.
  
  3. Print out the information for these Nmr.Shifts starting from the
       list of resonances in the Nmr.NmrProject.
  
  4. Create an Nmr.JCouplingList and create 5 Nmr.JCouplings, each
       linked to a different pair of resonances.
     
  5. Print out the information for these Nmr.JCouplings starting from
       the Nmr.JCouplingList object.


3. Nmr constraints

NMR constraints are stored in the NmrConstraints package, not the Nmr
package. However the system to assign constraints is the same as for
measurement lists, except that the classes are called
NmrConstraint.FixedResonance, FixedAtomSet and FixedResonanceSet.

Exercise 3.1:

  1. Create 20 new NmrConstraint.FixedResonances, half of them proton,
       the other half carbon.
  
  2. Create a DistanceConstraintList.
  
  3. Create 5 DistanceConstraints, each with 2
       DistanceConstraintItems. Try to use both targetValue/error and
       lowerLimit/upperLimit to set the distance bounds using typical
       NMR parameters.

     Also you will need to create DistanceConstraintItem objects with
       the correct resonances in them.
     
  4. Print out the distance and resonance information for these
       DistanceConstraints.
  
  5. Create a DihedralConstraintList.
  
  6. Create 5 DihedralConstraints, each with 2
       DihedralConstraintItems. The order of the connected resonances should
       be proton-carbon-carbon-proton.

     In this case, the resonances are in the main object, and the dihedral
       angle information is given in DihedralConstraintItem objects.  Again
       use typical NMR values of your choosing to populate the data in these
       items.
 
  7. Print out the angle and resonance information for these
       DihedralConstraints.
