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:edward.dauvergne@xxxxxxxxx]
Sent: Fri 11/10/2006 8:42 PM
To: Headey, Stephen
Cc: relax-users@xxxxxxx
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 <S.J.Headey@xxxxxxxxxxxx> 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']
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RE: problems reading Xeasy format