mailRe: "The unnumbered spin name 'H' already exists."


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Posted by Martin Ballaschk on February 01, 2013 - 15:38:
Hi Edward,

thank you for looking into it.

Why do you think a choosing function wouldn't be ok?

I guess in any case the user would have to decide for one of the possible 
locations anyway (also if neither reflects the "true" state of the protein in 
solution). If these alternate locations reflect interchanging conformations 
the "true" state must be both and neither, especially if there is no 
information on the timescale of the exchange. But then we can also ask to 
what extend data from PDB structure files reflect the true situation ...

Neither only one of the alternate locations, nor averaged positions would be 
perfect. I guess it would be good enough to cope with that by deciding on 
either of the positions and possibly re-run with the other position to see if 
it makes any difference. 

As a first workaround, I'll try to remove one of the conformations from the 
PDB files with the help of PyMol and work with the two versions seperately. 
(the parser from scipy possibly is also an option, but scipy fails to build 
on my mac)

Cheers
Martin

On 01.02.2013, at 13:18, "Edward d'Auvergne" <edward@xxxxxxxxxxxxx> wrote:
Hi Martin,

I've created a bug report for this problem at
https://gna.org/bugs/?20470.  The problem is that the 1OGT PDB entry
has alternate locations for a few residues - this is not a new bug but
a deficiency in the relax internal PDB parser.  I'm not sure what the
best solution would be in this case.  I might add the 'alt_loc'
argument to the structure.read_pdb user function to allow you to
choose one of the alternate locations, though I don't know if this is
the best solution.  What do you think?

Regards,

Edward



On 31 January 2013 18:21, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi,

That's a strange one!  I'll have to look at it tomorrow as I'm currently
waiting to board a plane at Lyon airport.

Cheers,

Edward

On Thursday, 31 January 2013, Martin Ballaschk wrote:

Hi Edward,

I have a strange problem (relax 2.1.2 @ Mac/Linux):

* create a data pipe inside relax (pipe.create)
* get 1OGT.pdb and load by
structure.read_pdb('./1OGT.pdb', read_mol=1)
* load amide nitrogens:
structure.load_spins(spin_id='@N', ave_pos=True)
* attach protons
sequence.attach_protons()

Now I get a very strange error message:
"RelaxError: The unnumbered spin name 'H' already exists."

But I didn't load a single proton before and there also is none in the PDB
file?

What do you think, what is going on?

Kind Regards,
Martin
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Martin Ballaschk
AG Schmieder
Leibniz-Institut für Molekulare Pharmakologie
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