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Hi Yufeng--
> My initial structure was generated from Cyana 2.0. I
> thought the error could arise from atom numbering
> mismatching, so spent a bit time managing to match the
> numbering of atoms in pdb and psf so that they are
> identical but the error is the same. So it could be
> the problem of my initial structure. But how do you
> define a decent structure? Any measures? I thought
> mine was good enough since it was folded, converged in
> structure calculation ...
it's probably fine, but this output:
> > > atoms:
> > > 1906 GLN 122 CD : { 10000, 10000, 10000 }
> > > 1909 GLN 122 HE21 : { 10000, 10000, 10000
> > }
> > > 1910 GLN 122 HE22 : { 10000, 10000, 10000
> > }
> > > 1907 GLN 122 OE1 : { 10000, 10000, 10000 }
> > > 1908 GLN 122 NE2 : { 10000, 10000, 10000 }
indicates that at least residue 122 contains some invalid atomic
positions. You might look at the input pdb to make sure these are
defined. Also, make sure that you really are reading in these
coordinates.
>
> BTW, do I have to add ANI pseudo-atoms to run
> refine.py against RDC data? If yes, how?
>
This is taken care of automatically by the anneal.py script. No need to
add these manually.
regards--
Charles
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