Re: Discrepancy for the cluster ID's saved in state an available in GUI. -- October 23, 2013

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 <edward@xxxxxxxxxxxxx>

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 <tlinnet@xxxxxxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>
>>
>> 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 <tlinnet@xxxxxxxxxxxxx>
>> wrote:
>> > Hi Edward.
>> >
>> > I still see the same behavior.
>> >
>> > Best
>> > Troels
>> >
>> >
>> > 2013/10/23 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >>
>> >> 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 <tlinnet@xxxxxxxxxxxxx>
>> >> 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
>> >> > relax-devel@xxxxxxx
>> >> >
>> >> > 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
>> >> >
>> >
>> >
>
>

Re: Discrepancy for the cluster ID's saved in state an available in GUI.

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