Calculating NMR observables with mdtraj.nmr()

MDTraj provides convenience functions for predicting various NMR observables such as chemical shifts. To do this, we provide wrapper functions for the SPARTA+, PPM, and ShiftX2 prediction algorithms.

In [1]:

%matplotlib inline
import mdtraj as md

Let's load a simple trajectory containing three identical frames of the villin headpiece protein.

In [2]:

trj = md.load("1vii_3frames.pdb", no_boxchk=True)

Now, let's calculate the chemical shifts with the program SPARTA+.

In [3]:

shifts = md.nmr.chemical_shifts_spartaplus(trj)
shifts[0:10]

/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/mdtraj/nmr/shift_wrappers.py:298: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  results.name[results.name == "HN"] = "H"

Out[3]:

	frame	0	1	2
resSeq	name
41	C	176.357	176.357	176.357
	CA	55.342	55.342	55.342
	CB	32.633	32.633	32.633
	HA	4.529	4.529	4.529
42	C	176.712	176.712	176.712
	CA	55.349	55.349	55.349
	CB	41.825	41.825	41.825
	H	8.738	8.738	8.738
	HA	4.518	4.518	4.518
	N	126.258	126.258	126.258

The data is returned as a Pandas Dataframe object. The rows correspond to the residue numbers and atom names, while each column corresponds to a different frame in your trajectory. Note that here our input had completely identical conformations in each frame, so we see identical values along each row.

(nmr.ipynb; nmr_eval.ipynb; nmr.py)