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" <[email protected]> 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 <[email protected]> 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 >>> [email protected] >>> >>> 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 [email protected] 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 [email protected] 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
