Helfrich Monte Carlo Flexible Fitting (HMFF)

see doi: https://doi.org/10.1101/2025.05.24.655915

Note: Only available in version 2.1 and beyond

Configuration

EnergyMethod = FreeDTS1.0_HMFF path xi theta_thr scaling offset [inversion] [step_size] [padding] [kernel] [percentile]

### Parameters

**Required parameters:**
- `path` - Path to CCP4/MRC file containing EM density data
- `xi` - Force scaling factor (typical: 1.0-50.0)
- `theta_thr` - Threshold value to exclude solvent contribution (typical: 0.0)
- `scaling` - Mesh scaling factor for distance/voxel conversion
- `offset` - Grid offset (single value or comma-separated x,y,z)

> **Note**: Vertex coordinates are transformed to voxel space as `(coord - offset) * sampling`, where `sampling=1/(scaling * voxel size)` using the voxel size from the MRC header.

**Optional parameters:**
- `inversion` - Invert density contrast (0=false, 1=true, default: 1)
- `step_size` - Step size along gradient (default: 0.0)
- `padding` - Scaling factor for boundary padding (default: 0.4)
- `kernel` - Gradient kernel size, must be odd (default: 3)
- `percentile` - theta_max determined as percentile of data (0.0-1.0, default: 0.999)

#### Usage Examples

**Basic usage:**

path.mrc 5.0 0 0.005 24.0

**Full parameter specification:**

path.mrc 5.0 0 0.005 24.0 1 0.0 0.4 3 0.999