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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