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

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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