Difference between revisions of "DPL94"

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The DPL94 model has the parameters {$R_{1\rho}'$, $...$, $\Phi_{ex}$, $k_{ex}$}.
 
The DPL94 model has the parameters {$R_{1\rho}'$, $...$, $\Phi_{ex}$, $k_{ex}$}.
 +
 +
=== Essentials ===
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It is essential to read in $R_{1\rho}'$ values before starting a calculation:
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<source lang="python">
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relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_values.txt', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
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</souce>
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 +
Where the data could be stored like
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<source lang="python">
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# mol_name    res_num    res_name    spin_num    spin_name    value  error 
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None              13          L        None            N 1.323940 0.146870
 +
None              15          R        None            N 1.344280 0.140560
 +
None              16          T        None            N 1.715140 0.136510
 +
</souce>
  
 
== Parameter name space in relax ==
 
== Parameter name space in relax ==

Revision as of 11:02, 5 March 2014

The Davis et al., 1994 2-site off-resonance fast exchange relaxation dispersion model for R1rho-type data. It extends the M61 model to off-resonance data, hence it collapses to this model for on-resonance data. The model is labelled as DPL94 in relax.

Equation

[math] \mathrm{R}_{1\rho}= \mathrm{R}_1\cos^2\theta + \left( \mathrm{R}_{1\rho}{´} + \frac{\Phi_\textrm{ex} \textrm{k}_\textrm{ex}}{\textrm{k}_\textrm{ex}^2 + \omega_\textrm{e}^2} \right) \sin^2\theta [/math]

Parameters

The DPL94 model has the parameters {$R_{1\rho}'$, $...$, $\Phi_{ex}$, $k_{ex}$}.

Essentials

It is essential to read in $R_{1\rho}'$ values before starting a calculation:

relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_values.txt', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
</souce>

Where the data could be stored like
<source lang="python">
# mol_name    res_num    res_name    spin_num    spin_name    value   error   
None               13           L        None            N 1.323940 0.146870
None               15           R        None            N 1.344280 0.140560
None               16           T        None            N 1.715140 0.136510
</souce>

== Parameter name space in relax ==
At time of writing (March 2014) the parameters in relax was stored as:
<source lang="python">
# Load the outcome from an analysis
state.load(state="results.bz2", dir="results/final")

# import spin functions
from pipe_control.mol_res_spin import return_spin, spin_loop

# Alias one spin
s13 = return_spin(":13@N")

# See attributes
dir(s13)

# See parameters
print(s13.params)
['r2', 'phi_ex', 'kex']

# Print parameters
print(s13.r2)
{'R1rho - 799.77739910 MHz': xx.yy}
print(s13.phi_ex)
print(s13.kex)

# See Ri data (ri_type:  The relaxation data type, i.e. 'R1', 'R2', 'NOE', or 'R2eff'. )
print(s13.ri_data)
{'R1': 1.3239399999999999}

# Print all spin id
for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False):
    if curspin.select == False:
        print(mol_name, res_num, res_name, spin_id)
    else:
        print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)

Reference

The reference for the DPL94 model is:

  • Davis, D., Perlman, M., and London, R. (1994). Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. J. Magn. Reson., 104(3), 266–275. (10.1006/jmrb.1994.1084)

Related models

The DPL94 model is simply the extension of the M61 model for off-resonance data.

Links

The implementation of the DPL94 model in relax can be seen in the:

See also