By looking at some old XEasy files generated using the commands 'tw' and 'le', I think I have tracked down the issue. In my files the proton is in the w1 columns and the nitrogen in the w2 columns. However in your file Steve, the proton and nitrogen are around the other way. I see two ways of overcoming this issue.
The first involves work on the part of the user. That would be to produce a file where the proton is in w1 and the nitrogen is in w2. However I don't like this approach - it should be relax doing all the work, not the user. The second solution would be for relax to use the supplied proton and nitrogen names (or the defaults if nothing is set) to determine which dimension is the proton and which is the nitrogen. This should be relatively easy to do. I'll start working on a solution. Cheers, Edward On 11/9/06, Stephen Headey <[EMAIL PROTECTED]> 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> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
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