Re: [bug #7676] xeasy data skipped when read -- November 10, 2006 - 07:33

Another problem that I've just seen is that relax assumes that the
first two lines of the file are header lines.  I'll have to fix that
issue as well.

Edward


On 11/9/06, Stephen Headey <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> URL:
>   <http://gna.org/bugs/?7676>
>
>                  Summary: xeasy data skipped when read
>                  Project: relax
>             Submitted by: sjheadey
>             Submitted on: Wednesday 11/08/2006 at 20:54
>                 Category: relax's source code
>                 Priority: 5 - Normal
>                 Severity: 4 - Important
>                   Status: None
>                  Privacy: Public
>              Assigned to: None
>          Originator Name:
>         Originator Email:
>              Open/Closed: Open
>                  Release: 1.2.8
>         Operating System: GNU/Linux
>
>     _______________________________________________________
>
> Details:
>
> My data is in Xeasy text window format and I specified format='xeasy' as
> instructed by the manual. This is recognised when the script is executed but
> only the first 2 lines of input appear to be read and the rest of the data is
> skipped. No NOE value is calculated for any residue.
>
> Here is a sample of the relevant input and output.
>
> INPUT
>
> 3    1   101.181   8.267    N  51 GLY     HN  51 GLY    9.578e+03  0.00e+00
>   m
> 5    1   103.383   8.211    N 148 GLY     HN 148 GLY    3.732e+03  0.00e+00
>   m
> 6    1   103.407   7.805    N 158 GLY     HN 158 GLY    1.425e+04  0.00e+00
>   m
> 8    1   103.257   8.593    N  88 GLY     HN  88 GLY    1.314e+04  0.00e+00
>   m
> 9    1   103.280   8.973    N 163 GLY     HN 163 GLY    1.745e+04  0.00e+00
>   m
>
> OUTPUT
> relax> noe.read(run='noe', file='ref.list', dir=None, spectrum_type='ref',
> format='xeasy', heteronuc='N', proton='HN', int_col=None)
> Reference spectrum.
> XEasy formatted data file.
>
> Opening the file 'ref.list' for reading.
> Skipping the data: ['6', '1', '103.407', '7.805', 'N', '158', 'GLY', 'HN',
> '158', 'GLY', '1.425e+04', '0.00e+00', 'm']
> Skipping the data: ['8', '1', '103.257', '8.593', 'N', '88', 'GLY', 'HN',
> '88', 'GLY', '1.314e+04', '0.00e+00', 'm']
> Skipping the data: ['9', '1', '103.280', '8.973', 'N', '163', 'GLY', 'HN',
> '163', 'GLY', '1.745e+04', '0.00e+00', 'm']
>
>
>     _______________________________________________________
>
> Follow-up Comments:
>
>
> -------------------------------------------------------
> Date: Wednesday 11/08/2006 at 20:54 By: Stephen Headey <Stephen Headey>
> My data is in Xeasy text window format and I specified format='xeasy' as
> instructed by the manual. This is recognised when the script is executed but
> only the first 2 lines of input appear to be read and the rest of the data is
> skipped. No NOE value is calculated for any residue.
>
> Here is a sample of the relevant input and output.
>
> INPUT
>
> 3    1   101.181   8.267    N  51 GLY     HN  51 GLY    9.578e+03  0.00e+00
>   m
> 5    1   103.383   8.211    N 148 GLY     HN 148 GLY    3.732e+03  0.00e+00
>   m
> 6    1   103.407   7.805    N 158 GLY     HN 158 GLY    1.425e+04  0.00e+00
>   m
> 8    1   103.257   8.593    N  88 GLY     HN  88 GLY    1.314e+04  0.00e+00
>   m
> 9    1   103.280   8.973    N 163 GLY     HN 163 GLY    1.745e+04  0.00e+00
>   m
>
> OUTPUT
> relax> noe.read(run='noe', file='ref.list', dir=None, spectrum_type='ref',
> format='xeasy', heteronuc='N', proton='HN', int_col=None)
> Reference spectrum.
> XEasy formatted data file.
>
> Opening the file 'ref.list' for reading.
> Skipping the data: ['6', '1', '103.407', '7.805', 'N', '158', 'GLY', 'HN',
> '158', 'GLY', '1.425e+04', '0.00e+00', 'm']
> Skipping the data: ['8', '1', '103.257', '8.593', 'N', '88', 'GLY', 'HN',
> '88', 'GLY', '1.314e+04', '0.00e+00', 'm']
> Skipping the data: ['9', '1', '103.280', '8.973', 'N', '163', 'GLY', 'HN',
> '163', 'GLY', '1.745e+04', '0.00e+00', 'm']
>
>
>
>
>
>
>     _______________________________________________________
>
> Carbon-Copy List:
>
> CC Address                          | Comment
> ------------------------------------+-----------------------------
> Available only the item webpage     | Submitted the item
>
>
>
>     _______________________________________________________
>
> File Attachments:
>
>
> -------------------------------------------------------
> Date: Wednesday 11/08/2006 at 20:54  Name: skipped.tar  Size: 270kB   By:
> sjheadey
> contains noe.py, xeasy text window peak internsity files, and a pdb
> <http://gna.org/bugs/download.php?file_id=1480>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?7676>
>
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