Re: [bug #20152] Import T1 demo.txt from DC to Relax -- September 07, 2012 - 08:42

Hi Mengjun,

I'm looking into this problem now, but one thing I noticed is that you
didn't set up the tryptophan indole NE1 spins.  Note that for your own
 analysis that you would need to set up these spins too.

Regards,

Edward



On 6 September 2012 23:00, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> URL:
>   <http://gna.org/bugs/?20152>
>
>                  Summary: Import T1 demo.txt from DC to Relax
>                  Project: relax
>             Submitted by: None
>             Submitted on: Thu 06 Sep 2012 09:00:04 PM UTC
>                 Category: GUI
>                 Severity: 3 - Normal
>                 Priority: 5 - Normal
>                   Status: None
>                  Privacy: Public
>              Assigned to: None
>          Originator Name:
>         Originator Email: mengjun.xue@xxxxxxxxxxxxxxxxxxxx
>              Open/Closed: Open
>          Discussion Lock: Any
>                  Release: 2.1.0
>         Operating System: Microsoft Windows
>
>     _______________________________________________________
>
> Details:
>
> Details:
>
> operating system: windows7
>
>
> version of Relax: 2.1.0
>
>
> operation steps:
>
>
> 1. start Relax_gui_mode.py
>
> 2. click new analysis
>
> 3. click model-free analysis
>
> 4. click next
>
> 5. click start
>
> 6. click spin viewer window
>
> 7. load 1UBQ_H.pdb
>
> 8. click next
>
> 9. choose The spin ID sting: @N
>
> 10. click next
>
> 11. click finish
>
> 12. click Add (bruker)
>
> 13.type 'r1_700' in the term of The relaxation data ID string
>
> 14. load the file 'T1 demo.txt'
>
> 15. click Next
>
>      relax 2.1.0
>
>                     Molecular dynamics by NMR data analysis
>
>                    Copyright (C) 2001-2006 Edward d'Auvergne
>               Copyright (C) 2006-2012 the relax development team
>
> This is free software which you are welcome to modify and redistribute under
> the conditions of the GNU General Public License (GPL).  This program,
> including all modules, is licensed under the GPL and comes with absolutely 
> no
> warranty.  For details type 'GPL' within the relax prompt.
>
> Assistance in using the relax prompt and scripting interface can be accessed
> by
> typing 'help' within the prompt.
>
> Processor fabric:  Uni-processor.
>
>
> relax> structure.read_pdb(file='C:UsersMengjun XueDesktopNew folder
> (3)1UBQ_H.pdb', dir=None, read_mol=None, set_mol_name=None, read_model=None,
> set_model_num=None, parser='internal')
>
> Internal relax PDB parser.
> Opening the file 'C:UsersMengjun XueDesktopNew folder (3)1UBQ_H.pdb' for
> reading.
> Adding molecule '1UBQ_H_mol1' to model None (from the original molecule 
> number
> 1 of model None)
>
> relax> structure.load_spins(spin_id='@N', ave_pos=True)
> Adding the following spins to the relax data store.
>
> # mol_name     res_num    res_name    spin_num    spin_name
> 1UBQ_H_mol1    1          MET         1           N
> 1UBQ_H_mol1    2          GLN         9           N
> 1UBQ_H_mol1    3          ILE         18          N
> 1UBQ_H_mol1    4          PHE         26          N
> 1UBQ_H_mol1    5          VAL         37          N
> 1UBQ_H_mol1    6          LYS         44          N
> 1UBQ_H_mol1    7          THR         53          N
> 1UBQ_H_mol1    8          LEU         60          N
> 1UBQ_H_mol1    9          THR         68          N
> 1UBQ_H_mol1    10         GLY         75          N
> 1UBQ_H_mol1    11         LYS         79          N
> 1UBQ_H_mol1    12         THR         88          N
> 1UBQ_H_mol1    13         ILE         95          N
> 1UBQ_H_mol1    14         THR         103         N
> 1UBQ_H_mol1    15         LEU         110         N
> 1UBQ_H_mol1    16         GLU         118         N
> 1UBQ_H_mol1    17         VAL         127         N
> 1UBQ_H_mol1    18         GLU         134         N
> 1UBQ_H_mol1    19         PRO         143         N
> 1UBQ_H_mol1    20         SER         150         N
> 1UBQ_H_mol1    21         ASP         156         N
> 1UBQ_H_mol1    22         THR         164         N
> 1UBQ_H_mol1    23         ILE         171         N
> 1UBQ_H_mol1    24         GLU         179         N
> 1UBQ_H_mol1    25         ASN         188         N
> 1UBQ_H_mol1    26         VAL         196         N
> 1UBQ_H_mol1    27         LYS         203         N
> 1UBQ_H_mol1    28         ALA         212         N
> 1UBQ_H_mol1    29         LYS         217         N
> 1UBQ_H_mol1    30         ILE         226         N
> 1UBQ_H_mol1    31         GLN         234         N
> 1UBQ_H_mol1    32         ASP         243         N
> 1UBQ_H_mol1    33         LYS         251         N
> 1UBQ_H_mol1    34         GLU         260         N
> 1UBQ_H_mol1    35         GLY         269         N
> 1UBQ_H_mol1    36         ILE         273         N
> 1UBQ_H_mol1    37         PRO         281         N
> 1UBQ_H_mol1    38         PRO         288         N
> 1UBQ_H_mol1    39         ASP         295         N
> 1UBQ_H_mol1    40         GLN         303         N
> 1UBQ_H_mol1    41         GLN         312         N
> 1UBQ_H_mol1    42         ARG         321         N
> 1UBQ_H_mol1    43         LEU         332         N
> 1UBQ_H_mol1    44         ILE         340         N
> 1UBQ_H_mol1    45         PHE         348         N
> 1UBQ_H_mol1    46         ALA         359         N
> 1UBQ_H_mol1    47         GLY         364         N
> 1UBQ_H_mol1    48         LYS         368         N
> 1UBQ_H_mol1    49         GLN         377         N
> 1UBQ_H_mol1    50         LEU         386         N
> 1UBQ_H_mol1    51         GLU         394         N
> 1UBQ_H_mol1    52         ASP         403         N
> 1UBQ_H_mol1    53         GLY         411         N
> 1UBQ_H_mol1    54         ARG         415         N
> 1UBQ_H_mol1    55         THR         426         N
> 1UBQ_H_mol1    56         LEU         433         N
> 1UBQ_H_mol1    57         SER         441         N
> 1UBQ_H_mol1    58         ASP         447         N
> 1UBQ_H_mol1    59         TYR         455         N
> 1UBQ_H_mol1    60         ASN         467         N
> 1UBQ_H_mol1    61         ILE         475         N
> 1UBQ_H_mol1    62         GLN         483         N
> 1UBQ_H_mol1    63         LYS         492         N
> 1UBQ_H_mol1    64         GLU         501         N
> 1UBQ_H_mol1    65         SER         510         N
> 1UBQ_H_mol1    66         THR         516         N
> 1UBQ_H_mol1    67         LEU         523         N
> 1UBQ_H_mol1    68         HIS         531         N
> 1UBQ_H_mol1    69         LEU         541         N
> 1UBQ_H_mol1    70         VAL         549         N
> 1UBQ_H_mol1    71         LEU         556         N
> 1UBQ_H_mol1    72         ARG         564         N
> 1UBQ_H_mol1    73         LEU         575         N
> 1UBQ_H_mol1    74         ARG         583         N
> 1UBQ_H_mol1    75         GLY         594         N
> 1UBQ_H_mol1    76         GLY         598         N
>
> relax> bruker.read(ri_id='r1_700', file='C:UsersMengjun XueDesktopNew folder
> (3)T1 demo.txt', dir=None)
> Opening the file 'C:UsersMengjun XueDesktopNew folder (3)T1 demo.txt' for
> reading.
> RelaxWarning: The spin '#1UBQ_H_mol1:1@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:2@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:3@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:4@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:5@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:6@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:7@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:8@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:9@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:10@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:11@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:12@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:13@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:14@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:15@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:16@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:17@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:18@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:19@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:20@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:21@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:22@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:23@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:24@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:25@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:26@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:27@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:28@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:29@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:30@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:31@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:32@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:33@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:34@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:35@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:36@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:37@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:38@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:39@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:40@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:41@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:42@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:43@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:44@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:45@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:46@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:47@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:48@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:49@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:50@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:51@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:52@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:53@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:54@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:55@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:56@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:57@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:58@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:59@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:60@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:61@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:62@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:63@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:64@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:65@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:66@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:67@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:68@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:69@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:70@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:71@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:72@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:73@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:74@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:75@N' is already named.  Set the force
> flag to rename.
> RelaxWarning: The spin '#1UBQ_H_mol1:76@N' is already named.  Set the force
> flag to rename.
> Traceback (most recent call last):
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0guiinterpreter.py", line 299, in run
>     apply(fn, args, kwds)
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0generic_fnsbruker.py", line 165, in read
>     rx = float(row[-2])
> ValueError: could not convert string to float: null
> Traceback (most recent call last):
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0guiwizard.py", line 682, in _go_next
>     self._display_page(self._current_page)
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0guiwizard.py", line 610, in _display_page
>     self._pages[i].on_display_post()
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0guicomponentsrelax_data.py", line 418, in
> wizard_update_int_type
>     page.uf_args['ri_id'].SetValue(value=id)
>   File "C:UsersMengjun XueDesktopdesk120816relax nmr
> abcrelax-2.1.0.Win32relax-2.1.0guiinput_elementsvalue.py", line 314, in
> SetValue
>     raise RelaxError("The Value element is read only, cannot set the value
> '%s'." % value)
> relax_errors.RelaxError: RelaxError: The Value element is read only, cannot
> set the value 'r1_700'.
>
>
>
>
>
>
>     _______________________________________________________
>
> File Attachments:
>
>
> -------------------------------------------------------
> Date: Thu 06 Sep 2012 09:00:04 PM UTC  Name: 1UBQ_H.pdb  Size: 122kB   By:
> None
>
> <http://gna.org/bugs/download.php?file_id=16482>
> -------------------------------------------------------
> Date: Thu 06 Sep 2012 09:00:04 PM UTC  Name: T1 demo.txt  Size: 61kB   By:
> None
>
> <http://gna.org/bugs/download.php?file_id=16483>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?20152>
>
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