Hi,
This error looks like a bug in relax. I haven't tested the back
calculation code for a little while, and I haven't noticed this
problem before. I do have a few ideas as to what the problem is but,
to help fix this issue, would you be able to create a bug report at
https://gna.org/bugs/?func=additem&group=relax? Thanks. It would be
very useful for debugging if you attached the PDB file as well. If
you could truncate this PDB file to a few residues, making sure the
truncated structure still gives the same error, that too would be
useful. If the PDB info is sensitive, the coordinates in the file can
simply be randomised.
Cheers,
Edward
On Tue, Mar 25, 2008 at 6:48 PM, Ryan MB Hoffman
<[EMAIL PROTECTED]> wrote:
> 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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