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 [ ]:%matplotlib inline import mdtraj as md
Let's load a simple trajectory containing three identical frames of the villin headpiece protein.
In [ ]:trj = md.load("1vii_3frames.pdb")
Now, let's calculate the chemical shifts with the program SPARTA+.
In [ ]:shifts = md.nmr.chemical_shifts_spartaplus(trj) shifts[0:10]
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.
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