Hi Edward.
I tried to generate sherekhan output, but since I have time_T2 of 0.04
and 0.06, for the two fields,
I cannot generate the input files for ShereKhan.
My problem origins from that I would like to compare results from Igor
Pro script.
Yet, another software solution.
I now got the expected pA values of 0.97 if I did a cluster of two residues.
If I do an initial Grid inc of 21, use
relax_disp.set_grid_r20_from_min_r2eff(force=False) I get this.
:10@N GRID r2600=20.28 r2500=18.48 dw=1.0 pA=0.900 kex=2000.80
chi2=28.28 spin_id=:10@N resi=10 resn=G
:10@N MIN r2600=19.64 r2500=17.88 dw=0.7 pA=0.500 kex=2665.16
chi2=14.61 spin_id=:10@N resi=10 resn=G
:10@N Clust r2600=18.43 r2500=16.98 dw=2.7 pA=0.972 kex=3831.77
chi2=48.79 spin_id=:10@N resi=10 resn=G
:11@N GRID r2600=19.54 r2500=17.96 dw=1.0 pA=0.825 kex=3500.65
chi2=47.22 spin_id=:11@N resi=11 resn=D
:11@N MIN r2600=14.98 r2500=15.08 dw=1.6 pA=0.760 kex=6687.15
chi2=18.36 spin_id=:11@N resi=11 resn=D
:11@N Clust r2600=18.19 r2500=17.31 dw=2.7 pA=0.972 kex=3831.77
chi2=48.79 spin_id=:11@N resi=11 resn=D
Ideally, I would like to cluster 68 residues.
But as you can see, if several of my residues start out with dw/pA far
from the Clustered result, this minimisation takes
hilarious long time.
I am very soon ready to send last fixes.
2014-04-29 19:19 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Troels,
Here is the new thread, just to keep things separate and clean. The
old thread that this originates from is at
http://thread.gmane.org/gmane.science.nmr.relax.devel/5402.
Note that you will always see different results for CPMGFit and all
other software when multiple field strength data is involved. The
reason is because of a fundamental assumption that that software
makes. And that is that R20 is the same for all fields! No other
dispersion software makes that assumption as it is know that the all
relaxation rates are field strength dependent. So comparing CPMGFit
to relax for debugging purposes is not of much use. See the CR72
model in test_suite/shared_data/dispersion/software_comparison for
example.
Are you sure that the CR72 model is suitable for this data? You could
try ShereKhan for a comparison as relax and ShereKhan, from all my
testing, produce 100% identical results. Or you could try the "MMQ
CR72" model in cpmg_fit from Dmitry Korzhnev. You could also compare
the numerical models to the CR72 model all within relax, as these
should produce similar results.
Regards,
Edward
On 29 April 2014 17:27, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
The problem is this:
For spin 10. After GRID search, and after minimisation.
GRID r2600=20.28 r2500=18.48 dw=1.7 pA=0.917 kex=6667.00 chi2=438.32
spin_id=:10@N resi=10 resn=G
MIN r2600=19.64 r2500=17.88 dw=0.7 pA=0.500 kex=2665.16 chi2=14.61
spin_id=:10@N resi=10 resn=G
I expect that pA should be between 0.95 and 0.99.
I also tried with cpmgfit:
# Parameter Fitted_Value Fitted_Error Sim_value
Sim_error
# R20 13.8014 0.6817 13.7140
0.4095
# papb 0.1134 1.0745 0.1071
0.0630
# dw 0.8920 4.2931 1.2044
0.6912
# kex 7.7524 0.5016 7.7358
0.4777
From:
relax_trunk/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/README
'Full_CPMG' or 'CR72' model parameter conversions.
==================================================
To convert from the papb parameter:
pA = 1.0 - papb
To obtain dw:
dw = 2.0 * pi * dw
And kex:
kex = kex * 1000
So cpmgfit gives pA=0.8866.
2014-04-29 16:58 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
Hi Edward.
I have some serious problems, that relax finds values of pA=0.5 after
minimisation.
This is in systemtest Relax_disp.test_sod1wt_t25_to_cr72
which I am working on.
These two support request, I think is essential for a better R1rho
inspection:
#3124 Grace graphs production for R1rho analysis with R2_eff as
function of Omega_eff
#3138 Interpolating theta through spin-lock offset [Omega], rather
than spin-lock field strength [w1]
But I don't have plans to work on them before I get the pA issues solved.
Anyway, maybe relax is in a good current state?
Best
Troels
2014-04-29 16:38 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,
I'm thinking about soon releasing relax 3.2.0 with all of the bug
fixes and the specific analysis API reorganisation and code cleanup.
Troels, do you have code lined up or plans which I should take into
account for this release?
Cheers,
Edward
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Re: pA = 0.5 problems.