Hi, This looks to be a genuine bug. If you could create a bug report, it would be much appreciated (see https://gna.org/bugs/?func=additem&group=relax). It would be useful to include the information from your mail. You could also attach the results file there, if you wish. Did you use the GUI for this, or a script for testing? It would be good to attach the output of running relax with teeing mode on (relax --tee log_file).
An ideal case would be if you created a set of test files which only include information for one or two spins which still reproduce the problem. That way I'll be able to easily reproduce the bug and come up with a solution within a few minutes (hopefully). Without the test data, I would have to spend a few hours or days trying to come up with a data set which triggers the bug. I could then also include this in the relax test suite to ensure that the problem never returns. The test data can be randomised for confidentiality, if needed. Cheers, Edward On 25 July 2012 14:27, Martin Ballaschk <[email protected]> wrote: > > Hi Edward, > > thank you for your quick response. Thanks also for your help. > > There's still a problem when trying to setup the dipole pair, maybe I messed > something up: > >> dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02e-10) >> Traceback (most recent call last): >> File "gui/interpreter.pyc", line 299, in run >> File "generic_fns/dipole_pair.pyc", line 237, in set_dist >> File "generic_fns/interatomic.pyc", line 234, in interatomic_loop >> KeyError: '#1shg-H_mol1:7@N' > > I don't really know what that means. > > Here's what I set up: > > > 1. Read @N spins from a relaxation output file, via the spin editor, works > nicely: > > relax> sequence.read(file='rx_t1.out', dir=None, spin_id_col=None, > mol_name_col=None, res_num_col=2, res_name_col=3, spin_num_col=None, > spin_name_col=5, sep=None, spin_id=None) > Opening the file 'rx_t1.out' for reading. > # mol_name res_num res_name spin_num spin_name > None 6 LYS None N > . > . > . > > > 2. Attach protons: > > relax> sequence.attach_protons() > > > 3. Set isotope and element types: > > relax> spin.isotope(isotope='15N', spin_id='@N', force=True) > > relax> spin.isotope(isotope='1H', spin_id='@H', force=True) > > relax> spin.element(element='N', spin_id=':*@N', force=True) > > 4. Define NH pairs: > > relax> dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) > Magnetic dipole-dipole interactions are now defined for the following spins: > > # Spin_ID_1 Spin_ID_2 > ':6@N' ':6@H' > ':7@N' ':7@H' > . > . > . > > 5. set the distance between N and H in the NH: > > relax> dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02e-10) > Traceback (most recent call last): > File "gui/interpreter.pyc", line 299, in run > File "generic_fns/dipole_pair.pyc", line 237, in set_dist > File "generic_fns/interatomic.pyc", line 234, in interatomic_loop > KeyError: '#1shg-H_mol1:7@N' > > So I don't know where this comes from. The NH pairs are set up, and > dipole_pair.set_dist takes just the three parameters. Oddly, relax does not > complain about the first residue (6), but the second in the sequence (7). > From how it shows up in the spin editor, there is actually no difference > between the two. > > The relax state can be found here, if you want to have a look: > https://www.dropbox.com/s/heukkeycpwzsvmb/state2.bz2 > > I'd appreciate your support :) > > Regards > Martin > > > On 24.07.2012, at 16:20, Edward d'Auvergne wrote: > >> Hi Martin, >> >> In the new relax versions, you'll have to do things a little >> differently. In the case where no structure is available, you can >> just click on the 'Skip' buttons for the structural parts of the >> dipolar relaxation wizard. I was thinking about having a page at the >> start of the wizard to ask if structural data is available, and use >> this to skip the 2 structure related wizard pages (structure.read_pdb >> and structure.get_pos), but it's a lot of effort considering most >> users will have a 3D structure. Note that you'll also have to have >> both proton and nitrogen spins set up in the new relax versions to >> define the magnetic dipole-dipole interaction. This will allow >> multi-pole relaxation support to be added to relax in the future. >> >> I hope this info helps. You may encounter other problems in the GUI >> if you don't have a structure. The flexibility of the scripting mode >> is lost in the GUI, so it is hard to bring back all the features into >> the GUI. But relax will handle an analysis without a structure. >> >> Regards, >> >> Edward >> >> >> >> On 24 July 2012 16:05, Martin Ballaschk <[email protected]> wrote: >>> Hi Edward, >>> >>> I was wondering if it is possible to run relaxGUI's model-free routine if >>> there is no structure model available. Of course, only the local_tm or >>> spherical "global" models could be used for an analysis, then. >>> >>> In the current 2.1.0 release, the user is forced to load a structure file >>> ("dipolar relaxation" button). Shouldn't relax run without loading any >>> structural information if I select "sphere" or "local_tm" in the protocol >>> mode field? Looking at the sample scripts in the manual, this could easily >>> be done via a relax script (I haven't tried), but is it possible also via >>> the GUI? >>> >>> Cheers >>> 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
