makevisualization

What makevisualization does?

It generates ChimeraX scripts (.cxc) based on a template script. Once you have the mapped positions or variants in the CSV files from the mapper command output, you can visualize your results in 3D using ChimeraX.

Input Data

• PDB Code ID(s) or PDB file(s).
• Interface and/or Structure mapping results generated by mapper in CSV format.

Input Arguments:

• -p or --pdb_code: PDB code/s to be found within the mapped file. If assembly is not included it will generate a script for all mapped assemblies of that PDB code.
• --pdb_list: Specifies that PDBs provided are in a file, separated by spaces, tabs, or new lines.
• -i or --interface_positions: File containing the variants mapped to interfaces generated by 3Dmapper.
• -s or --structure_positions: File containing the variants mapped to protein structure generated by 3Dmapper.
• -o or --output: Output folder in which the ChimeraX script/s will be saved.
• -n or --name: Base name for the ChimeraX scripts.
• -it or --inter_type: If interfaces are available, filter by specified interaction type (ligand, protein or nucleic).
• -l or --lighting: Select lighting option: full, soft or simple.
• -bg or --background: Select background option: white or black.
• -ns or --no_silhouette: Display will not present silhouettes.
• -mol or --mol_style: Select option for molecule style: ball, sphere, or stick.
• -is or --itf_style: Select option for molecule style of the interfaces displayed: ball, sphere, or stick.
• -f or --force: Force to overwrite?

Output

The program generates ChimeraX scripts (.cxc) that highlight the mapped interface variants in red and the rest of the structure in blue. It also colors the PDB chains per chain ID. One script is generated per selected PDB, allowing the user to focus on specific structures of interest. This feature helps to visualize the location of the mapped variants within the PDB structure and provides a better understanding of the impact of the variants on the protein function.