I'm trying to calculate R2s given a PDB and a diffusion tensor. I'm
getting the eigenvalues from another program. Below is a relax
session, edited only to compress some of the whitespace and with a
comment in square brackets.
Apparently I do calculate the XH vectors, with the 'pdb' command, but
they get forgotten somehow (or they aren't actually calculated). I'm
running relax 1.2.12.
relax> run.create('dummyMF','mf')
relax> pdb(run='dummyMF',file='buildX_0.pdb',dir='~/
workdir/',proton='HN')
Loading all structures from the PDB file.
Structure('/home/myuser/workdir/buildX_0.pdb'):
Peptide chain of length 180
Loading the sequence from the PDB file.
Calculating unit XH vectors.
Structure 1
RelaxWarning: The atom HN could not be found for residue 1
RelaxWarning: The atom HN could not be found for residue 53
RelaxWarning: The atom HN could not be found for residue 107
RelaxWarning: The atom HN could not be found for residue 108
[except for the N-terminus, the others are prolines, so the warnings
are ok]
Calculating the unit XH vectors from the structure.
relax> diffusion_tensor.init(run='dummyMF',params=
(2.405e06,2.463e06,7.986e06,80,80,60),param_types=2,fixed=1)
relax> model_free.create_model(run='dummyMF',model='m1',params=
['S2'],equation='mf_orig')
relax> relax_data.back_calc
(run='dummyMF',ri_label='R2',frq_label='800',frq=800.)
RelaxError: The unit XH bond vectors for the run 'dummyMF' have not
been calculated.
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