This is part of the isdb module

Calculates SAXS intensity.

SAXS intensities are calculated for a set of scattering vectors using QVALUE keywords numbered from 1. Form factors can be assigned either by polynomial expansion of any order by using the PARAMETERS keywords, or automatically matched to atoms using the ATOMISTIC flag by reading a PDB file. Alternatively to the atomistic representation, two types of coarse-grained mapping are available:

MARTINI.
ONEBEAD.

Whether for PARAMETERS, ATOMISTIC, and ONEBEAD the user must provide an all-atom PDB file via MOLINFO before the SAXS instruction. MARTINI requires a mapping scheme consisting of a PDB file that contains both the all-atom and MARTINI representations, and a bead position file (e.g., bead1: CENTER ATOMS=1,5,7,11,12 WEIGHTS=14,12,12, 12,16).

ONEBEAD scheme consists in a single-bead per amino acid residue or three-bead for nucleic acid residue (one for the phosphate group, one for the pentose sugar, one for the nucleobase). PLUMED creates a virtual bead on which the SAXS calculations are performed, centred on the COM of all atoms belonging to the bead. It is possible to account for the contribution of the solvation layer to the SAXS intensity by adding a correction term for the solvent accessible beads only: the form factors of the amino acids / phosphate groups / pentose sugars / nucleobases with a SASA (computed via LCPO algorithm) greater than a threshold are corrected according to an electron density term. Both the surface cut-off threshold and the electron density term can be set by the user with the SASA_CUTOFF and SOLVATION_CORRECTION keywords. Moreover, SASA stride calculation can be modified using SOLVATION_STRIDE, which is set to 100 steps by default. ONEBEAD requires an additional PDB file to perform mapping conversion, which must be provided via TEMPLATE keyword. This PDB file should only include the atoms for which the SAXS intensity will be computed. The AMBER OL3 (RNA) and OL15 (DNA) naming is required for nucleic acids. Two additional bead types are available for DNA and RNA besides phosphate group, pentose sugar, and nucleobase:

5'-end pentose sugar capped with an hydroxyl moiety at C5' (the residue name in the PDB must be followed by "5", e.g., DC5 or C5 for cytosine in DNA and RNA, respectively);
3'-end pentose sugar capped with an hydroxyl moiety at C3' (the residue name in the PDB must be followed by "3", e.g., DC3 or C3 for cytosine in DNA and RNA, respectively).

Experimental reference intensities can be added using the EXPINT keywords. All these values must be normalised to the SAXS intensity at q = 0. To facilitate this operation, the SCALE_EXPINT keyword can be used to provide the intensity at q = 0. Each EXPINT is divided by SCALE_EXPINT. The maximum QVALUE for ONEBEAD is set to 0.3 inverse angstroms. The solvent density, that by default is set to 0.334 electrons per cubic angstrom (bulk water), can be modified using the SOLVDENS keyword.

By default SAXS is calculated using Debye on CPU, by adding the GPU flag it is possible to solve the equation on a GPU if the ARRAYFIRE libraries are installed and correctly linked. METAINFERENCE can be activated using DOSCORE and the other relevant keywords.

Examples: in the following example the SAXS intensities are calculated using single-bead per residue approximation, with a SASA threshold of 1 square nanometer and a solvation term of 0.04. Each experimental intensity is divided by 1.4002, which is the corresponding theoretical intensity value at q = 0. The form factors are selected according to the PDB file specified by TEMPLATE keyword.

Click on the labels of the actions for more information on what each action computes

MOLINFO STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. 
=template_AA.pdb  You cannot view the components that are calculated by each action for this input file. Sorry 
SAXS: SAXS ...
   
   ATOMSThe atoms to be included in the calculation, e.g. =1-355 
   ONEBEAD( default=off ) calculate SAXS for a single bead model  
   TEMPLATEcompulsory keyword ( default=template.pdb )
A PDB file is required for ONEBEAD mapping =template_AA.pdb 
   SOLVDENScompulsory keyword ( default=0.334 )
Density of the solvent to be used for the correction of atomistic form factors =0.334 
   SOLVATION_CORRECTIONcompulsory keyword ( default=0.0 )
Hydration layer electron density correction (ONEBEAD only) =0.04 
   SOLVATION_STRIDEcompulsory keyword ( default=100 )
Number of steps between every new residues solvation estimation via LCPO (ONEBEAD
only) =1 
   SASA_CUTOFFcompulsory keyword ( default=1.0 )
SASA value to consider a residue as exposed to the solvent (ONEBEAD only) =1.0 
   SCALE_EXPINTcompulsory keyword ( default=1.0 )
Scaling value for experimental data normalization =1.4002 
   QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.03 EXPINT1Add an experimental value for each q value. =1.0902 
   QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.06 EXPINT2Add an experimental value for each q value. =0.790632 
   QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.09 EXPINT3Add an experimental value for each q value. =0.453808 
   QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.12 EXPINT4Add an experimental value for each q value. =0.254737 
   QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.15 EXPINT5Add an experimental value for each q value. =0.154928 
   QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.18 EXPINT6Add an experimental value for each q value. =0.0921503 
   QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.21 EXPINT7Add an experimental value for each q value. =0.052633 
   QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.24 EXPINT8Add an experimental value for each q value. =0.0276557 
   QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.27 EXPINT9Add an experimental value for each q value. =0.0122775 
   QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.30 EXPINT10Add an experimental value for each q value. =0.00880634 
... You cannot view the components that are calculated by each action for this input file. Sorry

PRINT ARG=(SAXS\.q-.*),(SAXS\.exp-.*) FILE=saxsdata STRIDE=1

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
score	the Metainference score
sigma	uncertainty parameter
sigmaMean	uncertainty in the mean estimate
neff	effective number of replicas
acceptSigma	MC acceptance for sigma values
q	the # SAXS of q

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
acceptScale	SCALEDATA	MC acceptance for scale value
acceptFT	GENERIC	MC acceptance for general metainference f tilde value
weight	REWEIGHT	weights of the weighted average
biasDer	REWEIGHT	derivatives with respect to the bias
scale	SCALEDATA	scale parameter
offset	ADDOFFSET	offset parameter
ftilde	GENERIC	ensemble average estimator
exp	EXPINT	the # experimental intensity

The atoms involved can be specified using

ATOMS

The atoms to be included in the calculation, e.g. the whole protein. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

NOISETYPE	( default=MGAUSS ) functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
LIKELIHOOD	( default=GAUSS ) the likelihood for the GENERIC metainference model, GAUSS or LOGN
DFTILDE	( default=0.1 ) fraction of sigma_mean used to evolve ftilde
SCALE0	( default=1.0 ) initial value of the scaling factor
SCALE_PRIOR	( default=FLAT ) either FLAT or GAUSSIAN
OFFSET0	( default=0.0 ) initial value of the offset
OFFSET_PRIOR	( default=FLAT ) either FLAT or GAUSSIAN
SIGMA0	( default=1.0 ) initial value of the uncertainty parameter
SIGMA_MIN	( default=0.0 ) minimum value of the uncertainty parameter
SIGMA_MAX	( default=10. ) maximum value of the uncertainty parameter
OPTSIGMAMEAN	( default=NONE ) Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
WRITE_STRIDE	( default=10000 ) write the status to a file every N steps, this can be used for restart/continuation
DEVICEID	( default=-1 ) Identifier of the GPU to be used
TEMPLATE	( default=template.pdb ) A PDB file is required for ONEBEAD mapping
DEUTER_CONC	( default=0. ) Fraction of deuterated solvent
SOLVDENS	( default=0.334 ) Density of the solvent to be used for the correction of atomistic form factors
SOLVATION_CORRECTION	( default=0.0 ) Hydration layer electron density correction (ONEBEAD only)
SASA_CUTOFF	( default=1.0 ) SASA value to consider a residue as exposed to the solvent (ONEBEAD only)
SOLVATION_STRIDE	( default=100 ) Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)
SCALE_EXPINT	( default=1.0 ) Scaling value for experimental data normalization

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
DOSCORE	( default=off ) activate metainference
NOENSEMBLE	( default=off ) don't perform any replica-averaging
REWEIGHT	( default=off ) simple REWEIGHT using the ARG as energy
SCALEDATA	( default=off ) Set to TRUE if you want to sample a scaling factor common to all values and replicas
ADDOFFSET	( default=off ) Set to TRUE if you want to sample an offset common to all values and replicas
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
GPU	( default=off ) calculate SAXS using ARRAYFIRE on an accelerator device
ATOMISTIC	( default=off ) calculate SAXS for an atomistic model
MARTINI	( default=off ) calculate SAXS for a Martini model
ONEBEAD	( default=off ) calculate SAXS for a single bead model
ARG	the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or . appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
AVERAGING	Stride for calculation of averaged weights and sigma_mean
SCALE_MIN	minimum value of the scaling factor
SCALE_MAX	maximum value of the scaling factor
DSCALE	maximum MC move of the scaling factor
OFFSET_MIN	minimum value of the offset
OFFSET_MAX	maximum value of the offset
DOFFSET	maximum MC move of the offset
REGRES_ZERO	stride for regression with zero offset
DSIGMA	maximum MC move of the uncertainty parameter
SIGMA_MEAN0	starting value for the uncertainty in the mean estimate
SIGMA_MAX_STEPS	Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used
TEMP	the system temperature - this is only needed if code doesn't pass the temperature to plumed
MC_STEPS	number of MC steps
MC_CHUNKSIZE	MC chunksize
STATUS_FILE	write a file with all the data useful for restart/continuation of Metainference
SELECTOR	name of selector
NSELECT	range of values for selector [0, N-1]
RESTART	allows per-action setting of restart (YES/NO/AUTO)
QVALUE	Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, .... You can use multiple instances of this keyword i.e. QVALUE1, QVALUE2, QVALUE3...
PARAMETERS	Used parameter Keywords like PARAMETERS1, PARAMETERS2. These are used to calculate the form factor for the \(i\)th atom/bead. You can use multiple instances of this keyword i.e. PARAMETERS1, PARAMETERS2, PARAMETERS3...
EXPINT	Add an experimental value for each q value. You can use multiple instances of this keyword i.e. EXPINT1, EXPINT2, EXPINT3...