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 <[EMAIL PROTECTED]> 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'] _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
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