Re: problems reading Xeasy format -- November 08, 2006 - 10:17

Hi,

Welcome to the relax-users mailing list.  Using your attached data
I've been able to replicate the issue.  I think I know what is
occurring, but relax's print out doesn't really tell you what the
issue is.  This can easily be fixed though.  Would you like to create
a bug report at https://gna.org/bugs/?group=relax for the issue?
Although not exactly a bug, the messages relax prints out could be
significantly improved.  The bug submission page, which you can access
from the 'bugs' menu item, is located at
https://gna.org/bugs/?func=additem&group=relax.  It's better to place
files within the bug tracker system rather than attaching large files
to a mailing list message - it makes it easier to access the files and
associate them with the correct bug.  Once the bug report is in place
we can start to sort out the issue (which I think is either an XEasy
'le' or swapped 1H-15N dimension problem).

Thanks,

Edward


On 11/8/06, Headey, Stephen <S.J.Headey@xxxxxxxxxxxx> wrote:
> Hi Edward,
>
> I've just started using relax and I thought I'd try calculating the NOE just 
> to try it out. 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. 
> What is the reason for this?
>
> Cheers,
> Steve Headey
>
> 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']
>
>
>
>
>
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