diff --git a/docs/_docs/running.md b/docs/_docs/running.md index feb84d6..9e7ad68 100644 --- a/docs/_docs/running.md +++ b/docs/_docs/running.md @@ -7,7 +7,7 @@ The class for running the PRE calculations is `PREpredict`. Here is how to calculate intensity ratios and PRE rates for a mutant of PDB 1NTI (20 conformations) using the rotamer-library approach ~~~ python -from DEERpredict.PRE import PREpredict +from DEERPREdict.PRE import PREpredict u = MDAnalysis.Universe('1nti.pdb') PRE = PREpredict(u, residue = 36, log_file = 'log', temperature = 298, atom_selection = 'H') @@ -44,7 +44,7 @@ Instead of using the rotamer library approach, the position of the unpaired elec setting `Cbeta=True`. ~~~ python -from DEERpredict.PRE import PREpredict +from DEERPREdict.PRE import PREpredict u = MDAnalysis.Universe('1nti.pdb') PRE = PREpredict(u, residue = 36, log_file = 'log', temperature = 298, atom_selection = 'H', Cbeta = True) @@ -57,7 +57,7 @@ PRE.run(output_prefix = 'calcPREs/res', tau_c = 2*1e-09, tau_t = .5*1e-9, delay Here is an example of how to run DEERpredict to calculate the DEER distribution for HIV-1 protease (PDB ID 3BVB) labeled with nitroxide groups at residue 55. ~~~ python -from DEERpredict.DEER import DEERpredict +from DEERPREdict.DEER import DEERpredict DEER = DEERpredict(MDAnalysis.Universe('3BVB.pdb'), residues = [55, 55], chains=['A', 'B'], log_file = 'log', temperature = 298 ) DEER.run(output_prefix = 'res') @@ -70,7 +70,7 @@ The function to back-calculate the time-domain data from a distance distribution The sums over the Boltzmann weights for the Lennard-Jones probe-protein interaction energies of positions K55 and K55' are saved to `res-Z-55-55.pkl`. ~~~ python -from DEERpredict.utils import Operations +from DEERPREdict.utils import Operations r, p = np.loadtxt('res-55-55.dat', unpack=True) t = np.linspace(0.01, 5.5, 512)