| relaxRatioPot | index relaxRatioPot.py |
relaxRatioPot:
Potential term to restrain observed ratios of residue specific NMR relaxation rates, r2/r1.
Creating a relaxRatioPot using Python user interface:
create_relaxRatioPot(name, data_in=None, Fr=None, sel = "known and (not resname ANI) and (not resname TEMP) and (not resname TRRP)",
= "known", temperature = 293, addAtoms=False, mass=1000, bond_type='NH')
returns a pointer to DiffPot object.
Defined in relaxRatioPot.py
name - is an instance name which later transferred to C++ constructor.
Fr - is frequency, in [MHz], of the spectrometer used to measure relaxation data.
sel - string specifying selection rules which is later transferred to
C++ constructor aud used to select atoms of the protein structure
accepted for calculations of protein diffusion tensor.
Could be left blank when calling this method.
Default value "known and (not resname ANI) and (not resname TEMP) and (not resname TRRP)"
means selection only the atoms with known coordinates excluding pseudo atoms
used by rdcPot and pseudo atoms used by diifPot and relaxRatioPot for
optimizing temperature. Must NOT be reevaluated later.
inc_sel - string specifying selection rules which will be used to select from supplied
relaxation data a sub set which will be used in structure elucidation protocol.
Could be left blank when calling this method.
Default value "known" means that all the supplied data will be used by the potential.
This selection operates on the level of Python only. The selected data then transferred
to the level of C++.
temperature - Temperature of water where protein tumbles.
if leaved blank when calling this method assumes the default value 293 K.
When this parameter is explicitly defined then the potential reevaluates
the factor accounting for viscosity and temperature of solvent, diffTmpF, for
given temperature, in Kelvins, assuming tumbling in water.
addAtoms - a parameter which specifies if it is necessary to create a set of pseudo atoms
which are used for temperature optimization. When lived blank then the default value
"False" is accepted; When assigned "True" value then the temperature atoms are created.
To be able to use these atoms for a non zero range for temperature optimization
should be specified using setRangeTmpFit() method. For details see below.
mass - mass of pseudo atoms. The default value 1000 [amu].
bond_type - a parameter used to select the strength of the dipolar coupling term and the value
of the ratio between gyromagnetic rations of interacting nucleii.
C++ constructor: relaxRatioPot(instanceName, sel, radii, sel_N, sel_HN, in_relax, in_relax_err):
instanceName - is a user-specified identifier of String type.
sel - is an AtomSel object specifying the atoms to include when
calculating the diffusion tensor.
radii - is a list of accepted values of van der Waals radii for atoms.
sel_N - is a CDSlist of Atom objects associated with Nitrogen atoms of HN pairs
for relaxation data accepted as experimental restraints for the potential.
sel_HN - is a CDSlist of Atom objects associated with Hydrogen atoms of HN pairs
for relaxation data accepted as experimental restraints for the potential.
in_relax - is a CDSlist of r2/r1 ratios.
in_relax_err - is a CDSlist of experimantal errors in r2/r1 ratios.
methods
calcEnergy() - calculates energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calculates energy and gradients, returns the energy value.
rms() - return the magnitude of violation of this
term -- abs(diff).
scale() - scale factor for this energy term.
scaleNHgrad() - additional scale factor for gradients of atoms in NH vectors.
Thus, the actual scale for NH vectors is scale()*scaleNHgrad().
scaleSAgrad() - additional scale factor for gradients of surface atoms.
Thus, the actual scale for NH vectors is scale()*scaleSAgrad().
diffShell() - hydration layer thickness.
diffTmpF() - factor which accounts for viscosity and temperature
of solvent.
diffRrmsd() - the value of rmsd separating current structure and
the one that was used for tessellation of the protein
surface last time which triggers new retessellation
of the protein surface.
diffRstep() - the number of derivatives calculations events which
triggers new retessellation of the protein surface.
selection() - return the atom selection specified in
the constructor.
NOTE! Selection should NOT be reevaluated after
initial setting the potential term. This would lead to
mismatching the arrays and total disaster.
get_rmsd() - calculates rmsd separating current structure and
the one that was used for tessellation of the protein
surface last time.
setScaleNHgrad(val) - sets additional scale factor for gradients of atoms in NH vectors.
setScaleSAgrad(val) - sets additional scale factor for gradients of surface atoms.
setMedianTmp(TmP) - sets nominal temperature.
getMedianTmp() - returns nominal temperature.
setRangeTmpFit(rangeTmpFit) - sets range of temperatures for temperature optimization.
rangeTmpFit() - returns the value of range of temperatures for temperature optimization.
curr_Tmp() - returns current value of temperature.
setFr(Fr) - sets spectrometer frequency.
getFr() - returns spectrometer frequency.
setgyroR(gyroR) - sets value of ratio between gyro magnetic
ratios of interacting nuclei.
getgyroR() - returns value of ratio between gyro magnetic
ratios of interacting nuclei.
setdipC2(dipC2) - stets the strength of dipole interaction.
getdipC2() - returns the strength of dipole interaction.
Diff_Tensor() - calculates components of diffusion tensor for
the current structure (in [10^-7 / s ]).
info() - current info about the state of this instance.
help() - this help.
The following parameters can be set [defaults in square brackets]
scale [1] - dimensionless.
setScaleNHgrad [1] - dimensionless.
setScaleSAgrad [1] - dimensionless.
diffShell [2.8] - Angstroms. Default value resembles a monolayer
of water molecules covering protein surface.
median_Tmp [293] - Kelvins. Default temperature.
rangeTmpFit [0] - Default range for temperature optimization.
diffTmpF [80315402327.6] - 1/s. Defult value corresponds to water at 293 K.
See definition below.
gyroR [9.869] - dimensionless. Default vale is for Ratio between
gyromagnetic rations of N and H nuclei.
dipC2 [1.2975] - [J^2/(s^2 T^2 m^6)]*[MHz^(-4)]. strength of the dipolar coupling interaction.
for a pair of a pair of NH nuclei
dipC2=(5/2)(gH*gN*h/(2*pi*rNH^3))^2;
where gyromagnetic rations
gH=267.5 [MHz/T]
gN=27.12 [MHz/T]
h=6.626e-34 [J s] Plank constant
rNH=1.02 [A] canonic distance between N and H nuclei
diffRrmsd [0.5] - Angstroms.
diffRstep [30] - dimensionless.
Fr[600] - MHz. Default spectrometer frequency.
The diffusion tensor is calculated using ellipsoid approximation derived from covariance matrix
for points of hydrated protein surface obtained as a result of tessellation.
The details of this method described in: Y. Ryabov, C. Geraghty, A. Varshney, and D. Fushman,
"An Efficient Computational Method for Predicting Rotational Diffusion Tensors of Globular Proteins
Using an Ellipsoid Representation", J. Am. Chem. Soc. 128: 15432-15444 (2006)
The subroutine for surface tessellation is build on the bases of surf program: A. Varshney, F.P.
Brooks Jr., W.V. Wright IEEE "Computing smooth molecular surfaces" Comput. Graphics Appl. 14: 19-25 (1994)
The temperature factor, diffTmpF, absorbs dependency of rotation diffusion parameters on temperature,
viscosity of solvent as well as some other constants and conversion factors.
diffTmpF defined as:
diffTmpF = (1.38e-23)*TmP/(16*P_I*eta_t*(1e-30))
where
1.38e-23, [J/K] - is Boltzmann constant.
PI = 3.14159265 - is irrational pi ratio between length of a circle and its diameter.
eta_t, [Pa s] - is viscosity of solvent.
TmP, [K] - is absolute temperature of solvent.
1e-30 - is a conversion factor between m^3 and A^3.
relaxRatioPot provides the facility to calculate diffTmpF for water at given temperature (see get_TmpF()).
This method uses empirical approximation for water viscosity temperature dependency from:
Weast, R.C. Handbook of Chemistry and Physics, 59th ed. CRC press West Palm Beach, FL 1978
dT=TmP-273;
eta_t=(1e-3)*(1.7753-0.0565*(dT)+1.0751e-3*(dT*dT)-9.2222e-6*(dT*dT*dT));
where
eta_t - is viscosity in Pa s
273 - is offset between Celsius and Klevin's temperature scales.
viscosity of water at 293 K (20 C): 1.002*(1e-3) [Pa s]
The energy function is defined as:
V = scale()* sacle_Lin() * rms()^2
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.
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| __package__ = None cvar = <Global variables> pyXplorHelp = Type help() for interactive help, or help(object) for help about object. tol_SB = 0.0001 | ||