Generate Polnet PNS file from PDB

This solution calls Membrane-Seg to Segment Membranes in Tomograms.

Arguments

--pdb_id

PDB ID for the Macromolecule to Model (default value: PARAMETER_VALUE)

--protein_name

Name of the Protein for the Associated PDB ID (default value: PARAMETER_VALUE)

--pdb_write_path

Folder Path for Where to Save the Downloaded PDB File (default value: PARAMETER_VALUE)

--mrc_write_path

Folder Path for Where to Save the Converted PDB file to MRC (default value: PARAMETER_VALUE)

--polnet_write_path

Folder Path for Where to Save the Converted MRC file for Polnet (default value: PARAMETER_VALUE)

--voxel_size

Voxel size per Ångström, scale of the tomogram resolution (default value: 10)

--resolution

Tomogram resolution in Ångströms. (default value: 30)

--mmer_iso

Isocontour (default value: 0)

--pmer_l

Flag to save segmentation scores. (default value: 1.1)

--pmer_occ

Flag to Save Inverted Segmentation Mask (default value: 0.2)

--pmer_over_tol

Overlappoing Tolerance (Percentage) (default value: 0.05)

--is_membrane

Indicate Protein Type (default value: 0)

--pmer_reverse_normals

Reverse membrane normal (For Membrane-Bound Protein) (default value: 0)

Please follow this link for details on how to install and run this solution.