Step 4. Results Visualization with ChimeraX

To visualize the mapping results obtained in Step 3, execute the following code:

makevisualization -p list_pdbs.txt --pdb_list -i ../3-mapper/3dmapper_results/csv/InterfacePositions_pident20.0_isoform_all_consequence_all.csv --force -s ../3-mapper/3dmapper_results/csv/StructurePositions_pident20.0_isoform_all_consequence_all.csv -is sphere

The generated Chimera scripts are here. Below you can visualize examples of the execution of two of the scripts.

Figure 1. PDB 2vyr with variants mapped to the interface (in red) and to the structure (in blue).

Figure 2. AlphaFold2 model O15151 with variants mapped to the structure (in blue) and chain colored in a red-blue gradient representing pLDDT scores (red, high pLDDT and blue low pLDDT).