Action: EMMIVOX
| Module | isdb |
|---|---|
| Description | Usage |
| Bayesian single-structure and ensemble refinement with cryo-EM maps. |   |
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 |
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 |
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 |
|---|---|---|---|
| ATOMS | input | none | atoms used in the calculation of the density map, typically all heavy atoms |
| DATA_FILE | compulsory | none | file with cryo-EM map |
| RESOLUTION | compulsory | none | cryo-EM map resolution |
| NORM_DENSITY | compulsory | none | integral of experimental density |
| WRITE_STRIDE | compulsory | none | stride for writing status file |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| NL_DIST_CUTOFF | optional | not used | neighbor list distance cutoff |
| NL_GAUSS_CUTOFF | optional | not used | neighbor list Gaussian sigma cutoff |
| NL_STRIDE | optional | not used | neighbor list update frequency |
| SIGMA_MIN | optional | not used | minimum density error |
| DBFACT | optional | not used | Bfactor MC step |
| BFACT_MAX | optional | not used | Bfactor maximum value |
| MCBFACT_STRIDE | optional | not used | Bfactor MC stride |
| BFACT_SIGMA | optional | not used | Bfactor sigma prior |
| STATUS_FILE | optional | not used | write a file with all the data useful for restart |
| SCALE | optional | not used | scale factor |
| OFFSET | optional | not used | offset |
| TEMP | optional | not used | temperature |
| WRITE_MAP | optional | not used | file with model density |
| WRITE_MAP_STRIDE | optional | not used | stride for writing model density to file |
| NO_AVER | optional | false | no ensemble averaging in multi-replica mode |
| CORRELATION | optional | false | calculate correlation coefficient |
| GPU | optional | false | calculate EMMIVOX on GPU with Libtorch |
| BFACT_NOCHAIN | optional | false | Do not use chain ID for Bfactor MC |
| BFACT_READ | optional | false | Read Bfactor on RESTART (automatic with DBFACT>0) |
| BFACT_MINIMIZE | optional | false | Accept only moves that decrease energy |
| MARTINI | optional | false | Use Martini scattering factors |