Re: Possible bug in relax -- December 01, 2009 - 15:18

Hi,

Ok, I'll wait.  I've noticed that u'u' is actually the 'u' character
in Unicode.  I'll definitely need more info to track this one down.
The key might be in the results files from the mf_multimodel.py
script.

Cheers,

Edward


2009/12/1 Olivier Serve <olivier.serve@xxxxxxxxx>:
> Dear Edward,
>        Thank you for answering so quickly. I will send you all details 
> tomorrow (It is night time for me now). But what I can say in the mean 
> time, is that : "RelaxError: The selection string u'u' is invalid" is the 
> full error message, quite short indeed, it took me long time to find this. 
> The modsel.py is almost same, I just use model 0 to 5, instead of 0 to 9. 
> But as I wrote in my previous mail, I am not at all sure that my solution 
> is pertinent.
>        I'll to send you a tar file tomorrow with all details.
>
> Have a nice day,
> Bye,
> Olivier Serve
> Olivier Serve
>
> Le 1 déc. 2009 à 22:40, Edward d'Auvergne a écrit :
>
> > Hi,
> >
> > I have a feeling that the problem lies elsewhere.  This change would
> > probably be fatal - are the models correctly selected?  Could you cut
> > and paste the full error message?  And maybe attach the modsel.py
> > script?  Without this, I'm not sure where the failure point is so I
> > don't know what the problem could be or what the cause is.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > 2009/12/1 Olivier Serve <olivier.serve@xxxxxxxxx>:
> > > Hi all,
> > >        I wrote possible bug in my title, because I am not sure yet it is 
> > > not my mistake. Here is my problem :
> > >        I ran smoothly all the following scripts : noe.py, relax-fit.py, 
> > > mf_multimodel.py. But when I ran the modsel.py, I got the following error 
> > > message : RelaxError: The selection string u'u' is invalid. (The name of 
> > > the molecule begins by 'u' (ubiquitin))
> > >        I tracked down the error (very deep) into relax : modsel.py -> 
> > > prompt/model_selection.Modsel -> 
> > > generic_func/model_selection.select->specific_fns/model_free/main.duplicate_data->generic_fns/sequence.generate->generic_fns/mol_res_spin.return_spin
> > >  at line 1879.
> > >        The code is the following : (selection is a selection string : 
> > > #<mol_name> :<res_id>[, <res_id>[, <res_id>, ...]] @<atom_id>[, 
> > > <atom_id>[, <atom_id>, ...]],)
> > >            if type(selection) == str:
> > >                selection = [selection]
> > >            select_obj = []
> > >            for i in range(len(selection)):
> > >                select_obj.append(Selection(selection[i]))
> > >
> > >        I think the problem here is that there is an iteration over a 
> > > selection string (something like #ubi....), so when the Selection 
> > > function sees 'u' alone, it does not mean anything and it raises the 
> > > error.
> > >        I turn the code into :
> > >                select_obj=Selection(selection)
> > >        And change the code accordingly a few lines after. The script 
> > > seemed to have run smoothly afterward.
> > >
> > >        If this is a bug, I'll be glad to open a bug report. If not, well, 
> > > I'll be glad to know what I am doing wrong.
> > >
> > > I wish all of you a nice day,
> > > Best regards,
> > > Olivier Serve
> > >
> > >
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> > >
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