Hi Edward, I couldn't reproduce the error with fresh data sets made on my linux machine. So this seems to be non-issue in the end ...
Cheers Martin On 25.07.2012, at 14:42, Edward d'Auvergne <[email protected]> wrote: > 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 -- 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
