Hi,
I perform CPMG-RD cluster fitting using relax, cluster refer to grouping
several residues (between 3 to 14 residues) for data from a 45 kDa protein. The
software is a good tool for doing this analysis. I marginally adjust the core
protocol with the header
"""Script for performing a full relaxation dispersion analysis using CPMG-type
data."""
I use only the CR72-model and I have a PRE_RUN_DIR from a run with individual
residues. I use duplicates for error estimation, on both the 800 MHz and 900
MHz data set, and AIC for model selection.
When I analyse the clustered data I’m curious to get R2eff_(back_calc) for each
data point. I clarify my main question by attaching some of my data.
###########
For residue 530, when I do individual fit I get this output.
From the log-file:
———
The spin cluster [':530@N'].
# Data pipe Num_params_(k) Num_data_sets_(n) Chi2
Criterion
No Rex - relax_disp 2 25 21.11216
25.11216
CR72 - relax_disp 5 25 13.93686
23.93686
The model from the data pipe 'CR72 - relax_disp' has been selected.
———
The file ‘disp_530_N.out’ in /final gives the following data table:
# Experiment_name Field_strength_(MHz) Disp_point_(Hz) R2eff_(measured)
R2eff_(back_calc) R2eff_errors
'SQ CPMG' 799.870000000 25.000000
17.523783179912268 16.953711340740483 0.831932502443187
'SQ CPMG' 799.870000000 50.000000
16.513029763549930 16.914478241596726 0.805586049587058
'SQ CPMG' 799.870000000 75.000000
16.920353186819355 16.875245142453196 0.816049323427317
'SQ CPMG' 799.870000000 100.000000
16.667402888129434 16.836012043882192 0.809527349094067
'SQ CPMG' 799.870000000 150.000000
16.454146002323920 16.757546676539960 0.804090431533660
'SQ CPMG' 799.870000000 200.000000
16.359623786385509 16.679111600438773 0.801698521274394
'SQ CPMG' 799.870000000 300.000000
15.525257427659495 16.523477804972345 0.781054888748662
'SQ CPMG' 799.870000000 350.000000
16.609858567997016 16.447662190184474 0.808054742944598
'SQ CPMG' 799.870000000 400.000000
16.844330710216166 16.374401478154368 0.814080812205130
'SQ CPMG' 799.870000000 500.000000
17.414128601521103 16.238705811895670 0.829011905615397
'SQ CPMG' 799.870000000 600.000000
16.093980388806685 16.120475644003818 0.795034804815920
'SQ CPMG' 799.870000000 800.000000
15.988036247232372 15.937187687218284 0.792401090807446
'SQ CPMG' 799.870000000 1000.000000
15.732649459437805 15.811741022120714 0.786107934589661
'SQ CPMG' 900.130000000 57.000000
19.386713898811351 20.163621643615215 0.801212497068354
'SQ CPMG' 900.130000000 114.000000
21.873502893081564 20.050473540803750 0.859660006101508
'SQ CPMG' 900.130000000 171.000000
19.133628964210569 19.937331394199191 0.795598311646227
'SQ CPMG' 900.130000000 228.000000
20.497316023709256 19.824330722189416 0.826567798566107
'SQ CPMG' 900.130000000 285.000000
20.091262254550443 19.712140304427066 0.817160298225920
'SQ CPMG' 900.130000000 400.000000
19.177817248045365 19.494278567900892 0.796574222459005
'SQ CPMG' 900.130000000 514.000000
19.111643299707755 19.300194513689348 0.795113430566997
'SQ CPMG' 900.130000000 628.000000
18.432363807026835 19.135138271300775 0.780352695478047
'SQ CPMG' 900.130000000 742.000000
19.383070346051138 18.999531230125285 0.801131245976946
'SQ CPMG' 900.130000000 857.000000
18.560791856291317 18.889165645990943 0.783110910382522
'SQ CPMG' 900.130000000 971.000000
18.810639108776328 18.801416118812085 0.788520121686263
'SQ CPMG' 900.130000000 1085.000000
18.943973311789268 18.730884832131551 0.791430360141496
###########
For a cluster fit (including residue 530) I get this output from the log-file:
———
The spin cluster [':530@N', ':536@N', ':537@N', ':538@N', ':550@N', ':551@N',
':552@N'].
# Data pipe Num_params_(k) Num_data_sets_(n) Chi2
Criterion
No Rex - relax_disp 14 175 458.66116
486.66116
CR72 - relax_disp 23 175 117.29418
163.29418
The model from the data pipe 'CR72 - relax_disp' has been selected.
———
But there is no corresponding data table.
###########
QUESTION 1:
Is it possible to get, or easily create a table with, in my case, 175
R2eff_(back_calc) for the cluster, so that I can get better resolution on the
Chi2 = 117.29418 above ?
And possibly study how a single residue affect the cluster fitting.
QUESTION 2:
Are there any reference to methods used for doing efficient selection of
residues included in the cluster? There is obviously an immense number of
combinations of residues to make clusters in a normal size protein. I consider
making a program/script for this process and would be curious to get some
inspiration.
Best regards
Johan Wallerstein, Sweden
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