Action: EMMIVOX
| Module | isdb |
|---|---|
| Description | Usage |
| Bayesian single-structure and ensemble refinement with cryo-EM maps. |   |
Details and examples
Bayesian single-structure and ensemble refinement with cryo-EM maps.
This action implements the Bayesian approach for single-structure and ensemble refinement from cryo-EM maps introduced here. EMMIVox does not require fitting the cryo-EM map with a Gaussian Mixture Model, as done in EMMI, but uses directly the voxels in the deposited map.
When run in single-replica mode, this action allows atomistic, flexible refinement (and B-factors inference) of an individual structure into a density map. A coarse-grained forward model can also be used in combination with the MARTINI force field. Combined with a multi-replica framework (such as the -multi option in GROMACS), the user can model an ensemble of structures using the Metainference approach that is introduced in the paper cited below. The approach can be used to model continous dynamics of flexible regions as well as semi-ordered waters, lipids, and ions.
installing libtorch
To use EMMIVOX, PLUMED must be linked against the LibTorch library using the instructions on the module page.
Examples
Complete tutorials for single-structure and ensemble refinement can be found here.
Input
The 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 |
|---|---|---|
| ATOMS | atoms | atoms used in the calculation of the density map, typically all heavy atoms |
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 |
|---|---|---|---|
| scoreb | scalar | default | Bayesian score |
| scale | scalar | default | scale factor |
| offset | scalar | default | offset |
| accB | scalar | default | Bfactor MC acceptance |
| kbt | scalar | default | temperature in energy unit |
| corr | scalar | CORRELATION | correlation coefficient |
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ATOMSThis keyword do not have examples | input | none | atoms used in the calculation of the density map, typically all heavy atoms |
| DATA_FILEThis keyword do not have examples | compulsory | none | file with cryo-EM map |
| RESOLUTIONThis keyword do not have examples | compulsory | none | cryo-EM map resolution |
| NORM_DENSITYThis keyword do not have examples | compulsory | none | integral of experimental density |
| WRITE_STRIDEThis keyword do not have examples | compulsory | none | stride for writing status file |
| NUMERICAL_DERIVATIVESThis keyword do not have examples | optional | false | calculate the derivatives for these quantities numerically |
| NOPBCThis keyword do not have examples | optional | false | ignore the periodic boundary conditions when calculating distances |
| NL_DIST_CUTOFFThis keyword do not have examples | optional | not used | neighbor list distance cutoff |
| NL_GAUSS_CUTOFFThis keyword do not have examples | optional | not used | neighbor list Gaussian sigma cutoff |
| NL_STRIDEThis keyword do not have examples | optional | not used | neighbor list update frequency |
| SIGMA_MINThis keyword do not have examples | optional | not used | minimum density error |
| DBFACTThis keyword do not have examples | optional | not used | Bfactor MC step |
| BFACT_MAXThis keyword do not have examples | optional | not used | Bfactor maximum value |
| MCBFACT_STRIDEThis keyword do not have examples | optional | not used | Bfactor MC stride |
| BFACT_SIGMAThis keyword do not have examples | optional | not used | Bfactor sigma prior |
| STATUS_FILEThis keyword do not have examples | optional | not used | write a file with all the data useful for restart |
| SCALEThis keyword do not have examples | optional | not used | scale factor |
| OFFSETThis keyword do not have examples | optional | not used | offset |
| TEMPThis keyword do not have examples | optional | not used | temperature |
| WRITE_MAPThis keyword do not have examples | optional | not used | file with model density |
| WRITE_MAP_STRIDEThis keyword do not have examples | optional | not used | stride for writing model density to file |
| NO_AVERThis keyword do not have examples | optional | false | no ensemble averaging in multi-replica mode |
| CORRELATIONThis keyword do not have examples | optional | false | calculate correlation coefficient |
| GPUThis keyword do not have examples | optional | false | calculate EMMIVOX on GPU with Libtorch |
| BFACT_NOCHAINThis keyword do not have examples | optional | false | Do not use chain ID for Bfactor MC |
| BFACT_READThis keyword do not have examples | optional | false | Read Bfactor on RESTART (automatic with DBFACT>0) |
| BFACT_MINIMIZEThis keyword do not have examples | optional | false | Accept only moves that decrease energy |
| MARTINIThis keyword do not have examples | optional | false | Use Martini scattering factors |
References
More information about how this action can be used is available in the following articles: