Action: SAXS
| Module | isdb |
|---|---|
| Description | Usage |
| Calculates SAXS intensity. |   |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| score | scalar | default | the Metainference score |
| sigma | scalar | default | uncertainty parameter |
| sigmaMean | scalar | default | uncertainty in the mean estimate |
| neff | scalar | default | effective number of replicas |
| acceptSigma | scalar | default | MC acceptance for sigma values |
| acceptScale | scalar | SCALEDATA | MC acceptance for scale value |
| acceptFT | scalar | GENERIC | MC acceptance for general metainference f tilde value |
| weight | scalar | REWEIGHT | weights of the weighted average |
| biasDer | scalar | REWEIGHT | derivatives with respect to the bias |
| scale | scalar | SCALEDATA | scale parameter |
| offset | scalar | ADDOFFSET | offset parameter |
| ftilde | scalar | GENERIC | ensemble average estimator |
| q | scalar | default | The # SAXS of q |
| exp | scalar | EXPINT | The # experimental intensity |
Input
The arguments and atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ARG | scalar | the labels of the values from which the function is calculated |
| ATOMS | atoms | The atoms to be included in the calculation, e |
Further details and examples
Text from manual goes here
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ARG | input | none | the labels of the values from which the function is calculated |
| ATOMS | input | none | The atoms to be included in the calculation, e |
| NOISETYPE | compulsory | MGAUSS | functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) |
| LIKELIHOOD | compulsory | GAUSS | the likelihood for the GENERIC metainference model, GAUSS or LOGN |
| DFTILDE | compulsory | 0.1 | fraction of sigma_mean used to evolve ftilde |
| SCALE0 | compulsory | 1.0 | initial value of the scaling factor |
| SCALE_PRIOR | compulsory | FLAT | either FLAT or GAUSSIAN |
| OFFSET0 | compulsory | 0.0 | initial value of the offset |
| OFFSET_PRIOR | compulsory | FLAT | either FLAT or GAUSSIAN |
| SIGMA0 | compulsory | 1.0 | initial value of the uncertainty parameter |
| SIGMA_MIN | compulsory | 0.0 | minimum value of the uncertainty parameter |
| SIGMA_MAX | compulsory | 10. | maximum value of the uncertainty parameter |
| OPTSIGMAMEAN | compulsory | NONE | Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly |
| WRITE_STRIDE | compulsory | 10000 | write the status to a file every N steps, this can be used for restart/continuation |
| DEVICEID | compulsory | -1 | Identifier of the GPU to be used |
| TEMPLATE | compulsory | template.pdb | A PDB file is required for ONEBEAD mapping |
| DEUTER_CONC | compulsory | 0. | Fraction of deuterated solvent |
| SOLVDENS | compulsory | 0.334 | Density of the solvent to be used for the correction of atomistic form factors |
| SOLVATION_CORRECTION | compulsory | 0.0 | Solvation layer electron density correction (ONEBEAD only) |
| SASA_CUTOFF | compulsory | 1.0 | SASA value to consider a residue as exposed to the solvent (ONEBEAD only) |
| N | compulsory | 10 | Number of points in the resolution function integral |
| SOLVATION_STRIDE | compulsory | 10 | Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only) |
| SCALE_EXPINT | compulsory | 1.0 | Scaling value for experimental data normalization |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| DOSCORE | optional | false | activate metainference |
| NOENSEMBLE | optional | false | don't perform any replica-averaging |
| REWEIGHT | optional | false | simple REWEIGHT using the ARG as energy |
| AVERAGING | optional | not used | Stride for calculation of averaged weights and sigma_mean |
| SCALEDATA | optional | false | Set to TRUE if you want to sample a scaling factor common to all values and replicas |
| SCALE_MIN | optional | not used | minimum value of the scaling factor |
| SCALE_MAX | optional | not used | maximum value of the scaling factor |
| DSCALE | optional | not used | maximum MC move of the scaling factor |
| ADDOFFSET | optional | false | Set to TRUE if you want to sample an offset common to all values and replicas |
| OFFSET_MIN | optional | not used | minimum value of the offset |
| OFFSET_MAX | optional | not used | maximum value of the offset |
| DOFFSET | optional | not used | maximum MC move of the offset |
| REGRES_ZERO | optional | not used | stride for regression with zero offset |
| DSIGMA | optional | not used | maximum MC move of the uncertainty parameter |
| SIGMA_MEAN0 | optional | not used | starting value for the uncertainty in the mean estimate |
| SIGMA_MAX_STEPS | optional | not used | Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used |
| TEMP | optional | not used | the system temperature - this is only needed if code doesn't pass the temperature to plumed |
| MC_STEPS | optional | not used | number of MC steps |
| MC_CHUNKSIZE | optional | not used | MC chunksize |
| STATUS_FILE | optional | not used | write a file with all the data useful for restart/continuation of Metainference |
| FMT | optional | not used | specify format for HILLS files (useful for decrease the number of digits in regtests) |
| SELECTOR | optional | not used | name of selector |
| NSELECT | optional | not used | range of values for selector [0, N-1] |
| RESTART | optional | not used | allows per-action setting of restart (YES/NO/AUTO) |
| NOPBC | optional | false | Ignore the periodic boundary conditions when calculating distances |
| SERIAL | optional | false | Perform the calculation in serial - for debug purpose |
| GPU | optional | false | Calculate SAXS using ARRAYFIRE on an accelerator device |
| ABSOLUTE | optional | false | Absolute intensity: the intensities for each q-value are not normalised for the intensity at q=0 |
| ATOMISTIC | optional | false | Calculate SAXS for an atomistic model |
| MARTINI | optional | false | Calculate SAXS for a Martini model |
| ONEBEAD | optional | false | calculate SAXS for a single bead model |
| QVALUE | optional | not used | Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, |
| PARAMETERS | optional | not used | Used parameter Keywords like PARAMETERS1, PARAMETERS2 |
| PARAMETERSFILE | optional | not used | Read the PARAMETERS from a file |
| EXPINT | optional | not used | Add an experimental value for each q value |
| SIGMARES | optional | not used | Variance of Gaussian distribution describing the deviation in the scattering angle for each q value |