Hi Edward. I can confirm that the problem does not exist on windows. :-)
I will try again on linux. This reminds me of an earlier bug, where I also updated the files, but had the same problem. But some tries later, it was gone. Hm. But thanks! 2013/10/23 Edward d'Auvergne <[email protected]> > Ok, I'm pretty sure there is a problem on your side. I tested this on > Windows Vista, Windows 7, Mac OS X 10.7, and two different Linux > systems. On one Linux system I tested it with Python 2.5, 2.6, and > 2.7, using different wxPython 2.8 or 2.9 combinations. In all cases, > the 'model_cluster' entry was present in the drop-down menu. So I > selected that and the spin ":4@N" in the second element and clicked on > ok. Then in the prompt GUI window, I saw: > > relax> cdp.clustering > {'free spins': [':5@N', ':6@N'], 'model_cluster': [':2@N', ':3@N', ':4@N > ']} > relax> > > I could see this on all systems. Before the commit: > > ------------------------------------------------------------------------ > r21219 | bugman | 2013-10-23 16:08:26 +0200 (Wed, 23 Oct 2013) | 7 lines > Changed paths: > M /branches/relax_disp/specific_analyses/relax_disp/api.py > > Fix for the relaxation dispersion specific private _cluster_ids() method. > > This was identified at > http://thread.gmane.org/gmane.science.nmr.relax.devel/4716. > > The cluster data structure was not being referenced correctly. > ------------------------------------------------------------------------ > > I could also not see 'model_cluster' in the drop-down menu, only 'free > spins', but after the change on all systems I can see both. So I > really cannot for the life of me work out why you cannot see > 'model_cluster' in the drop-down menu :S > > Regards, > > Edward > > > On 23 October 2013 18:23, Troels Emtekær Linnet <[email protected]> > wrote: > > I am on redhat linux. > > > > uname -a > > Linux haddock 2.6.32-358.18.1.el6.x86_64 #1 SMP Fri Aug 2 17:04:38 EDT > 2013 > > x86_64 x86_64 x86_64 GNU/Linux > > > > in relax: > > import wx > > wx.__version__ > > '2.8.12.0' > > > > ------------ > > Hardware information: > > Machine: x86_64 > > Processor: x86_64 > > Endianness: little > > Total RAM size: 24013 Mb > > Total swap size: 26191 Mb > > > > Operating system information: > > System: Linux > > Release: 2.6.32-358.18.1.el6.x86_64 > > Version: #1 SMP Fri Aug 2 17:04:38 EDT 2013 > > GNU/Linux version: Red Hat Enterprise Linux Server 6.4 Santiago > > Distribution: redhat 6.4 Santiago > > Full platform string: > > Linux-2.6.32-358.18.1.el6.x86_64-x86_64-with-redhat-6.4-Santiago > > > > Python information: > > Architecture: 64bit ELF > > Python version: 2.6.6 > > Python branch: tags/r266 > > Python build: r266:84292, May 27 2013 05:35:12 > > Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-3) > > Libc version: glibc 2.2.5 > > Python implementation: CPython > > Python revision: 84292 > > Python executable: /usr/bin/python > > Python flags: sys.flags(debug=0, py3k_warning=0, > > division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0, > > dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, > > tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0) > > Python float info: sys.floatinfo(max=1.7976931348623157e+308, > > max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, > > min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16, > > radix=2, rounds=1) > > Python module path: ['/sbinlab2/software/NMR-relax/relax_disp', > > '/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python', > > '/net/tomat/home/tlinnet/kte/t1rho_NCBD/Original_data/relax', > > '/sbinlab2/software/x64/haddock2.1', > > '/sbinlab2/software/x64/lib64/python2.6/site-packages', > > '/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/python', > '/usr/lib64/python26.zip', > > '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', > > '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', > > '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages', > > '/usr/lib64/python2.6/site-packages/gst-0.10', > > '/usr/lib64/python2.6/site-packages/gtk-2.0', > > '/usr/lib64/python2.6/site-packages/webkit-1.0', > > '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode', > > '/usr/lib/python2.6/site-packages', > > '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info'] > > > > Python packages and modules (most are optional): > > > > Name Installed Version Path > > minfx True 1.0.5 > > /usr/lib/python2.6/site-packages/minfx > > bmrblib True 1.0.3 > > /usr/lib/python2.6/site-packages/bmrblib > > numpy True 1.4.1 > > /usr/lib64/python2.6/site-packages/numpy > > scipy True 0.7.2 > > /usr/lib64/python2.6/site-packages/scipy > > wxPython True 2.8.12.0 (gtk2-unicode) > > /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx > > mpi4py True 1.3.1 > > /usr/lib64/python2.6/site-packages/mpi4py > > epydoc False > > optparse True 1.5.3 > > /usr/lib64/python2.6/optparse.pyc > > readline True > > /usr/lib64/python2.6/lib-dynload/readline.so > > profile True > > /usr/lib64/python2.6/profile.pyc > > bz2 True > > /usr/lib64/python2.6/lib-dynload/bz2.so > > gzip True > > /usr/lib64/python2.6/gzip.pyc > > io True > > /usr/lib64/python2.6/io.pyc > > xml True 0.8.4 (PyXML) > > /usr/lib64/python2.6/site-packages/_xmlplus/__init__.pyc > > xml.dom.minidom True > > /usr/lib64/python2.6/site-packages/_xmlplus/dom/minidom.pyc > > > > relax information: > > Version: repository checkout > > Processor fabric: Uni-processor. > > > > relax C modules: > > > > Module Compiled File type > > Path > > target_functions.relax_fit True ELF 64-bit LSB shared object, > > x86-64, version 1 (SYSV), dynamically linked, not stripped > > /sbinlab2/software/NMR-relax/relax_disp/target_functions/relax_fit.so > > > > > > > > > > 2013/10/23 Edward d'Auvergne <[email protected]> > >> > >> Hmmm, very strange. I just repeated your steps and managed to add the > >> spin ":4" to 'model_cluster'. I cannot see the problem on my system. > >> Which OS are you on and which wxPython version are you using? I might > >> have to test this on a different OS! > >> > >> Cheers, > >> > >> Edward > >> > >> > >> > >> On 23 October 2013 18:04, Troels Emtekær Linnet <[email protected]> > >> wrote: > >> > Hi Edward. > >> > > >> > Version is: > >> > 21219 > >> > > >> > If I do this in the prompt: > >> > -------- > >> > pipe.create(pipe_name='test', bundle='test', pipe_type='relax_disp') > >> > > >> > spin.create(spin_name='N', spin_num=1, res_name='V', res_num=2, > >> > mol_name=None) > >> > spin.create(spin_name='N', spin_num=2, res_name='F', res_num=3, > >> > mol_name=None) > >> > spin.create(spin_name='N', spin_num=3, res_name='G', res_num=4, > >> > mol_name=None) > >> > spin.create(spin_name='N', spin_num=4, res_name='R', res_num=5, > >> > mol_name=None) > >> > spin.create(spin_name='N', spin_num=5, res_name='C', res_num=6, > >> > mol_name=None) > >> > > >> > relax_disp.cluster('model_cluster', ':2@N') > >> > relax_disp.cluster('model_cluster', ':3@N') > >> > --------- > >> > > >> > cdp.clustering > >> > {'free spins': [':4@N', ':5@N', ':6@N'], 'model_cluster': [':2@N', > >> > ':3@N']} > >> > > >> > Open Data Pipe Editor (Ctrl+d) > >> > Right click the pipe, and click "Associate with new auto-analysis". > >> > > >> > The "free spins, model_cluster" is in the line. > >> > > >> > But if I Click "Cluster button", I cannot assign new spin ids to > >> > 'model_cluster' > >> > since that label is not available in the dropdown. > >> > > >> > > >> > 2013/10/23 Edward d'Auvergne <[email protected]> > >> >> > >> >> This is strange. In the relax_disp branch I started the GUI with: > >> >> > >> >> $ relax -g > >> >> > >> >> Then started a new dispersion analysis, opened the prompt window and > >> >> typed: > >> >> > >> >> relax> cdp.clustering = { > >> >> 'free spins': [':5@N', ':9@N', ':11@N', ':12@N', ':13@N', ':14@N', > >> >> ':25@N', ':31@N', ':33@N', ':39@N', ':42@N', ':80@N', ':87@N', > >> >> ':89@N', ':90@N', ':111@N', ':121@N'], > >> >> 'model_cluster': [':2@N', ':3@N', ':4@N', ':6@N', ':7@N', ':8@N', > >> >> ':10@N', ':15@N', ':16@N', ':17@N', ':18@N', ':19@N', ':20@N', > >> >> ':21@N', ':22@N', ':23@N', ':26@N', ':27@N', ':28@N', ':29@N', > >> >> ':30@N', ':32@N', ':34@N', ':35@N', ':36@N', ':37@N', ':38@N', > >> >> ':40@N', ':41@N', ':43@N', ':44@N', ':45@N', ':46@N', ':48@N', > >> >> ':49@N', ':50@N', ':51@N', ':52@N', ':54@N', ':55@N', ':56@N', > >> >> ':57@N', ':58@N', ':59@N', ':60@N', ':61@N', ':62@N', ':63@N', > >> >> ':64@N', ':65@N', ':66@N', ':67@N', ':68@N', ':72@N', ':73@N', > >> >> ':74@N', ':75@N', ':76@N', ':77@N', ':78@N', ':81@N', ':82@N', > >> >> ':83@N', ':84@N', ':85@N', ':91@N', ':92@N', ':93@N', ':94@N', > >> >> ':95@N', ':96@N', ':97@N', ':98@N', ':99@N', ':100@N', ':101@N', > >> >> ':104@N', ':105@N', ':106@N', ':107@N', ':109@N', ':110@N', ':112@N > ', > >> >> ':113@N', ':114@N', ':115@N', ':116@N', ':118@N', ':120@N', ':122@N > ', > >> >> ':123@N', ':124@N', ':125@N', ':127@N', ':129@N'] > >> >> } > >> >> > >> >> Then when I click on the 'Cluster' button in the GUI, I can select > >> >> both the 'free spins' and 'model_cluster'. Maybe I was a bit fast > >> >> with the email. Could you update your code again, check that you > have > >> >> r21219, and then see if the problem is still there? > >> >> > >> >> Cheers, > >> >> > >> >> Edward > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> On 23 October 2013 17:24, Troels Emtekær Linnet < > [email protected]> > >> >> wrote: > >> >> > Hi Edward. > >> >> > > >> >> > I still see the same behavior. > >> >> > > >> >> > Best > >> >> > Troels > >> >> > > >> >> > > >> >> > 2013/10/23 Edward d'Auvergne <[email protected]> > >> >> >> > >> >> >> Hi Troels, > >> >> >> > >> >> >> This does look like it is an issue. I think I have located the > >> >> >> problem to the _cluster_ids() method in > >> >> >> specific_analyses/relax_disp/api.py. At least I fixed a bug in > that > >> >> >> method. Could you check again to see if it is fixed? > >> >> >> > >> >> >> Cheers, > >> >> >> > >> >> >> Edward > >> >> >> > >> >> >> > >> >> >> > >> >> >> On 22 October 2013 19:34, Troels Emtekær Linnet > >> >> >> <[email protected]> > >> >> >> wrote: > >> >> >> > Hi Edward. > >> >> >> > > >> >> >> > Before I do a clustering analysis, I often prepare the data in > >> >> >> > scripts, > >> >> >> > save > >> >> >> > the state, and then > >> >> >> > inspect the setup in the GUI. > >> >> >> > > >> >> >> > I open the relax saved state. > >> >> >> > Open the Data Pipe Editor (Ctrl+d) > >> >> >> > Right click the pipe, and click "Associate with new > >> >> >> > auto-analysis". > >> >> >> > > >> >> >> > If I open the prompt (Ctrl+p), and write > >> >> >> > cdp.clustering > >> >> >> > > >> >> >> > I get > >> >> >> > { > >> >> >> > 'free spins': [':5@N', ':9@N', ':11@N', ':12@N', ':13@N', > ':14@N', > >> >> >> > ':25@N', > >> >> >> > ':31@N', ':33@N', ':39@N', ':42@N', ':80@N', ':87@N', ':89@N', > >> >> >> > ':90@N', > >> >> >> > ':111@N', ':121@N'], > >> >> >> > 'model_cluster': [':2@N', ':3@N', ':4@N', ':6@N', ':7@N', ':8@N > ', > >> >> >> > ':10@N', > >> >> >> > ':15@N', ':16@N', ':17@N', ':18@N', ':19@N', ':20@N', ':21@N', > >> >> >> > ':22@N', > >> >> >> > ':23@N', ':26@N', ':27@N', ':28@N', ':29@N', ':30@N', ':32@N', > >> >> >> > ':34@N', > >> >> >> > ':35@N', ':36@N', ':37@N', ':38@N', ':40@N', ':41@N', ':43@N', > >> >> >> > ':44@N', > >> >> >> > ':45@N', ':46@N', ':48@N', ':49@N', ':50@N', ':51@N', ':52@N', > >> >> >> > ':54@N', > >> >> >> > ':55@N', ':56@N', ':57@N', ':58@N', ':59@N', ':60@N', ':61@N', > >> >> >> > ':62@N', > >> >> >> > ':63@N', ':64@N', ':65@N', ':66@N', ':67@N', ':68@N', ':72@N', > >> >> >> > ':73@N', > >> >> >> > ':74@N', ':75@N', ':76@N', ':77@N', ':78@N', ':81@N', ':82@N', > >> >> >> > ':83@N', > >> >> >> > ':84@N', ':85@N', ':91@N', ':92@N', ':93@N', ':94@N', ':95@N', > >> >> >> > ':96@N', > >> >> >> > ':97@N', ':98@N', ':99@N', ':100@N', ':101@N', ':104@N', > ':105@N', > >> >> >> > ':106@N', > >> >> >> > ':107@N', ':109@N', ':110@N', ':112@N', ':113@N', ':114@N', > >> >> >> > ':115@N', > >> >> >> > ':116@N', ':118@N', ':120@N', ':122@N', ':123@N', ':124@N', > >> >> >> > ':125@N', > >> >> >> > ':127@N', ':129@N'] > >> >> >> > } > >> >> >> > > >> >> >> > But if I click the "Cluster" button, The cluster ID > >> >> >> > "model_cluster'", > >> >> >> > is > >> >> >> > not > >> >> >> > available from the drop-down list. > >> >> >> > > >> >> >> > Should this be fixed? > >> >> >> > > >> >> >> > Best > >> >> >> > Troels > >> >> >> > > >> >> >> > _______________________________________________ > >> >> >> > relax (http://www.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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