| This is part of the isdb module |
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 [21] . The approach can be used to model continous dynamics of flexible regions as well as semi-ordered waters, lipids, and ions.
- Warning
- To use EMMIVOX, PLUMED must be linked against the LibTorch library as described here
- Examples
Complete tutorials for single-structure and ensemble refinement can be found here.
- 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 |
| scoreb | Bayesian score |
| scale | scale factor |
| offset | offset |
| accB | Bfactor MC acceptance |
| kbt | temperature in energy unit |
In addition the following quantities can be calculated by employing the keywords listed below
| Quantity | Keyword | Description |
| corr | CORRELATION | correlation coefficient |
- The atoms involved can be specified using
| ATOMS | atoms used in the calculation of the density map, typically all heavy atoms. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- Compulsory keywords
| DATA_FILE | file with cryo-EM map |
| RESOLUTION | cryo-EM map resolution |
| NORM_DENSITY | integral of experimental density |
| WRITE_STRIDE | stride for writing status file |
- Options
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
| NO_AVER | ( default=off ) no ensemble averaging in multi-replica mode |
| CORRELATION | ( default=off ) calculate correlation coefficient |
| GPU | ( default=off ) calculate EMMIVOX on GPU with Libtorch |
| BFACT_NOCHAIN | ( default=off ) Do not use chain ID for Bfactor MC |
| BFACT_READ | ( default=off ) Read Bfactor on RESTART (automatic with DBFACT>0) |
| BFACT_MINIMIZE | ( default=off ) Accept only moves that decrease energy |
| MARTINI | ( default=off ) Use Martini scattering factors
|
| NL_DIST_CUTOFF | neighbor list distance cutoff |
| NL_GAUSS_CUTOFF | neighbor list Gaussian sigma cutoff |
| NL_STRIDE | neighbor list update frequency |
| SIGMA_MIN | minimum density error |
| DBFACT | Bfactor MC step |
| BFACT_MAX | Bfactor maximum value |
| MCBFACT_STRIDE | Bfactor MC stride |
| BFACT_SIGMA | Bfactor sigma prior |
| STATUS_FILE | write a file with all the data useful for restart |
| SCALE | scale factor |
| OFFSET | offset |
| TEMP | temperature |
| WRITE_MAP | file with model density |
| WRITE_MAP_STRIDE | stride for writing model density to file |
1.8.17