Hi Edward.
I would like to hear, if you could give some hints how you would
handle a clustering analysis situation the best way.
It is related to this entry, which I am modifying.
http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Execute_a_clustering_analysis
I would like to do the clustering analysis for the model: TSMFK01
When I do the clustering analysis, I am pointing to a previous result
directory.
I am clustering those residues, which is not the model "No Rex".
relax will read the file TSMFK01/kAB.out file with the previous results.
I will take the averaged kAB values for the residues specified in the cluster.
-------------
# Parameter description: The exchange rate from state A to state B.
#
# mol_name res_num res_name spin_num spin_name value
error
None 3 A 1 N
1060772.86091342 None
None 4 E 2 N
3.20195659408987 None
None 5 F 3 N
2.15902319384803 None
None 6 D 4 N
2.7190458578948 None
None 7 K 5 N
2.37325031348072 None
None 8 A 6 N
828438.809437978 None
None 9 A 7 N
2.93391757645135 None
...
--------------
The problem here is, that it seems that the fitting is going "crazy"
for some residues.
And the averaged starting value will be:
Averaged k_AB value: 83471.18......
The expected value would be somewhere: kAB = 2-10
What would be the best solution for this problem?
1) Modify the source code for the TSMFK01 model, so results are within
expected range.
2) Manually modify the TSMFK01/kAB.out and write k_AB=5
3) Skipping the pointing to a previous run directory, loop over the
spins and setting kAB=5 before doing a minimization?
-----------------
Output from an auto-analysis
-------------------------
-----------------------
- The 'TSMFK01' model -
-----------------------
relax> pipe.copy(pipe_from='base pipe', pipe_to='TSMFK01',
bundle_to='relax_disp')
relax> pipe.switch(pipe_name='TSMFK01')
relax> relax_disp.select_model(model='TSMFK01')
The Tollinger et al. (2001) 2-site very-slow exchange model, range of
microsecond to second time scale.
relax> value.copy(pipe_from='R2eff', pipe_to='TSMFK01', param='r2eff')
relax> pipe.create(pipe_name='pre', pipe_type='relax_disp', bundle=None)
relax> results.read(file='results',
dir='/net/tomat/home/tlinnet/kte/acbp/acbp_cpmg_disp_04MGuHCl_40C_041223_RELAX.fid/relax_reprocess/model_sel_analyt/TSMFK01')
Opening the file
'/net/tomat/home/tlinnet/kte/acbp/acbp_cpmg_disp_04MGuHCl_40C_041223_RELAX.fid/relax_reprocess/model_sel_analyt/TSMFK01/results.bz2'
for reading.
relax> relax_disp.parameter_copy(pipe_from='pre', pipe_to='TSMFK01')
Copying parameters for the spin block [':3@N', ':4@N', ':5@N', ':6@N',
':7@N', ':9@N', ':10@N', ':11@N', ':12@N', ':13@N', ':14@N', ':15@N',
':16@N', ':17@N', ':18@N', ':20@N', ':21@N', ':22@N', ':23@N',
':24@N', ':25@N', ':26@N', ':27@N', ':28@N', ':29@N', ':30@N',
':31@N', ':32@N', ':33@N', ':34@N', ':35@N', ':36@N', ':37@N',
':38@N', ':39@N', ':40@N', ':41@N', ':43@N', ':45@N', ':46@N',
':47@N', ':48@N', ':49@N', ':50@N', ':52@N', ':53@N', ':54@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', ':69@N',
':70@N', ':71@N', ':72@N', ':73@N', ':74@N', ':75@N', ':77@N',
':78@N', ':80@N', ':81@N', ':82@N', ':83@N', ':84@N', ':85@N',
':86@N']
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Averaged k_AB value: 83471.182642624335131
relax> pipe.switch(pipe_name='TSMFK01')
relax> pipe.delete(pipe_name='pre')
relax> minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None,
max_iter=10000000, constraints=True, scaling=True, verbosity=1)
Best
Troels
Troels Emtekær Linnet
The best way to handle a cluster analysis