Hi Edward, The problem is with my understanding of Subversion. This just downloads updates, right? Do I install relax-1.2.9, for example in /usr/local/software and then go to /usr/local/software/relax-1.2.9 and type the following?
svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2 and then svn up Am I best ignoring the 1.3 update at present? Please give idiot-proof instructions. Otherwise my insistance that the problem is not fixed may be wrongly interpreted as subversion. Cheers, Steve -----Original Message----- From: Edward d'Auvergne [mailto:[EMAIL PROTECTED] Sent: Wed 11/15/2006 3:19 PM To: Headey, Stephen Cc: [email protected] Subject: Re: problems reading Xeasy format That's bizarre. When I run the 'noe.py' from the tar file script attached to bug #7676 (https://gna.org/bugs/?7676), after renaming '3c14.pdb' to 'ark.pdb', 'ref.list' to 'ref2.text', and 'sat.list' to 'sat2.text', both the 1.2 and 1.3 repository lines work fine and I get grace plots of your steady-state NOE values. For 1.3, the 'noe.py' script had to be modified as the 1.2 version user function 'pdb()' is currently called 'pdb.read()' in the 1.3 line (this will change again soon). When I tried the 1.2.9 version, all the data from the XEasy files was skipped - this is understandable though as this version doesn't contain the fixes. One thing that it might be is that your working copy of the repository source code may be out of date. This can be updated by typing 'svn up' in the relax base directory. I'm not sure what is going on because I can't reproduce the error. Are you using the same data as attached to the bug report? Any help in reproducing this bug would be appreciated. Cheers, Edward On 11/14/06, Headey, Stephen <[EMAIL PROTECTED]> wrote: > Hi Edward, > > I've installed relax-1.2.9. I've also installed subversion and used it to > get relax-1.2 and relax-1.3 as you specified using the commands > > svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2 > svn co svn://svn.gna.org/svn/relax/1.2 relax-1.3 > > Everything seemed to download OK. However, the same (or similar) problems > are still occurring. Did I neglect something? The ref data set is still > skipped, the sat file is not read and I get the following error: > > Skipping the data: ['660', '1', '123.588', '8.445', 'N', '181', 'LYS', > 'HN', '181', 'LYS', '5.754e+04', '0.00e+00', 'm'] > Skipping the data: ['661', '1', '127.440', '8.029', 'N', '182', 'GLN', > 'HN', '182', 'GLN', '9.641e+04', '0.00e+00', 'm'] > Traceback (most recent call last): > File "/usr/local/bin/relax", line 454, in ? > Relax() > File "/usr/local/bin/relax", line 166, in __init__ > self.interpreter.run() > File "/usr/local/relax/prompt/interpreter.py", line 213, in run > run_script(intro=self.relax.intro_string, local=self.local, > script_file=self.relax.script_file, quit=1) > File "/usr/local/relax/prompt/interpreter.py", line 388, in run_script > console.interact(intro, local, script_file, quit) > File "/usr/local/relax/prompt/interpreter.py", line 340, in > interact_script > execfile(script_file, local) > File "noe.py", line 11, in ? > noe.read(name, file='ref.list_ori', spectrum_type='ref', > format='xeasy') > File "/usr/local/relax/prompt/noe.py", line 226, in read > self.__relax__.specific.noe.read(run=run, file=file, dir=dir, > spectrum_type=spectrum_type, format=format, heteronuc=heteronuc, > proton=proton, int_col=int_col) > File "/usr/local/relax/specific_fns/noe.py", line 110, in read > self.relax.generic.intensity.read(run=run, file=file, dir=dir, > format=format, heteronuc=heteronuc, proton=proton, int_col=int_col, > assign_func=self.assign_function) > File "/usr/local/relax/generic_fns/intensity.py", line 142, in read > res_num, X_name, H_name, intensity = self.intensity(file_data[i]) > File "/usr/local/relax/generic_fns/intensity.py", line 73, in > intensity_xeasy > if line[4] == 'inv.': > IndexError: list index out of range > > Cheers, > Steve > > > > > -----Original Message----- > From: Edward d'Auvergne [mailto:[EMAIL PROTECTED] > Sent: Fri 11/10/2006 8:42 PM > To: Headey, Stephen > Cc: [email protected] > Subject: Re: problems reading Xeasy format > > 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 > > > > > > > > > > > > _______________________________________________ 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
