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In this module you can select a series of parameters that can be saved in a comma-separated file (extension .csv) at the end of the hydrodynamic computations. The module consists of six, tab-selectable screens where the parameters are subdivided according to their origin and characteristics. The parameters can be toggled from one window of the panel to the other (left side, list of parameters available; right side, parameters to be saved) by clicking on them (multiple selection available; you can scroll down while keeping pressed the central mouse button to select a contiguos series of parameters) and then using the arrows present between the two windows.
The six screens are Main hydro results:, Additional SMI results:, Additional ZENO results:, Additional GRPY results:, Solvent conditions:, and ASA results:. Note that the order by which you select the parameters (i.e. the order by which they appear in the right-side window) will be their order in the saved file. The Model name "parameter" is the only one which is fixed, alwas available and not selectable, because it will be used to distinguish the results of individual models when multiple models (such as from NMR-style files) are analyzed in a single run.
The Main hydro results: screen contains all parameters which are listed in the Show Hydrodynamic Calculations pop-up window, plus some other general parameters i.e.:
Total beads in model
Used beads in model
Molecular mass [Da]
Partial specific volume [cm^3/g]
Sedimentation coefficient s [S]
Translational diffusion coefficient D [cm^2/sec]
Stokes radius [nm]
Translational frictional coefficient [g/s]
Frictional ratio
Relaxation time tau(h) [ns]
Intrinsic viscosity [cm^3/g]
Radius of gyration [nm] (from bead model)
Used beads volume [nm^3]
Used beads surface area [nm^2]
Used bead mass [Da]
Total surface area of beads in the model [nm^2]
Total volume of beads in the model [nm^3]
Number of unused beads (this differs from what is reported in the *.hydro_res file because the used beads are already listed in the Main hydro results panel)
Conversion Factor
Processing time [s]
Maximum extensions [X, Y, Z]
Axial ratios [X:Z, X:Y, Y:Z]
The Additional SMI results: screen contains all the other parameters which are reported in the *.hydro_res file:
Centre of resistance [X, Y, Z] [nm] (X, Y, Z coordinates saved)
Centre of mass [X, Y, Z] [nm] (X, Y, Z coordinates saved)
Centre of diffusion [X, Y, Z] [nm] (X, Y, Z coordinates saved)
The Additional ZENO results: screen contains parameters that are calculated only by the ZENO method, like the standard deviations (s.d.), obtained from the averages of many blocks of independent runs:
Sedimentation coefficient s.d.
Translational diffusion coefficient D s.d.
Stokes radius s.d.
Translational frictional coefficient s.d.
Frictional ratio s.d.
Intrisic viscosity s.d.
Dt/d0
Dt/d0 s.d.
Dimensionless intrinsic viscosity [eta]
Dimensionless intrinsic viscosity s.d.
The Additional GRPY results: screen contains additional parameters that are calculated by the GRPY method:
Rotational frictional coefficient [g*cm^2/s]
Rotational diffusion coefficient [1/s]
Rotational frictional coefficent [X, Y, Z] [g*cm^2/s]
Rotational diffusion coefficent [X, Y, Z] [1/s]
Rotational Stokes' radius [X, Y, Z] [nm]
Relaxation times, tau(1) [ns]
Relaxation times, tau(2) [ns]
Relaxation times, tau(3) [ns]
Relaxation times, tau(4) [ns]
Relaxation times, tau(5) [ns]
Relaxation times, tau(m) [ns]
GRPY Einstein's radius [nm]
The Solvent conditions: screen contains the parameters as set in the
Hydrodynamic Calculations options module:
Solvent name
Solvent acronym
Solvent Temperature [°C]
Solvent viscosity [cP]
Solvent density [g/ml]
pH
The ASA results: screen presently contains only two parameters, derived from the ASAB1 execution:
Radius of gyration (+r) [A] (from PDB atomic structure) (computed by taking into account the actual radius r of each atom)
Radius of gyration (-r) [A] (from PDB atomic structure) (computed without taking into account the actual radius r of each atom)
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Last modified on December 18, 2020.