Re: problems reading Xeasy format -- November 10, 2006 - 08:43

I've now fixed the issue.  Steve reported the problem as bug #7676
(https://gna.org/bugs/index.php?7676), and the fine details of the fix
are available at that link.  The problem was that relax was assuming
that the w1 dimension in the XEasy text file was the proton dimension.
There was also a side issue that the first two lines of the XEasy
file were being ignored.  I have fixed the problems by creating two
new functions: one to determine how many header lines are in the file;
the other to determine which of w1 or w2 is the proton dimension.

To get the new code there are two options.  The changes are located in
the relax source code repository (http://svn.gna.org/viewcvs/relax/)
which is a Subversion repository (http://subversion.tigris.org/).  The
exact location of the fixes are the 1.2 and 1.3 repository lines.
Steve, if you have Subversion installed, you can download the 1.2 line
code by typing:

svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2

If that doesn't work, you can also use the command:

svn co http://svn.gna.org/svn/relax/1.2 relax-1.2

This code is very stable.  The other option is to wait until I make a
new relax release.  As I have just released versions 1.2.8 and 1.2.9
(please don't use 1.2.8 as that version introduced a very important
bug) in the last week, I would prefer to wait a while before releasing
1.2.10 to accumulate a few more bug fixes.

Cheers,

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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