Hi, No need to remove conformations - I've already implemented a fix. The solution is the addition of the 'alt_loc' argument to the structure.read_pdb user function. If alternate location indicators are present in the PDB and the 'alt_loc' argument has not been specified, then a RelaxError will occur. Otherwise, only the records matching the 'alt_loc' argument will be read (well, only when the alternate location indicator PDB field has a value). You might need to wait a little while though as I'm still debugging this.
Regards, Edward On 1 February 2013 15:38, Martin Ballaschk <[email protected]> wrote: > 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 _______________________________________________ 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
