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> _______________________________________________ Message sent via/by Gna! http://gna.org/