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
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
--
Martin Ballaschk
AG Schmieder
Leibniz-Institut für Molekulare Pharmakologie
Robert-Rössle-Str. 10
13125 Berlin
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
Büro: A 1.26
Labor: C 1.10
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
Re: "The unnumbered spin name 'H' already exists."