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In this video tutorial, the speaker shows how to obtain a PDB file for a specific small molecule. They begin by suggesting to open a Google window and type the name of the molecule, in this case, "curcumin pubchem." They click on the website that appears and navigate to the download tab on the right-hand side. Clicking on this tab allows them to download a 3D conformer of the molecule in an SDF file format. Next, they recommend using an SDF to PDB file converter. They suggest searching for an online smiles translator, which offers different options. They demonstrate how to select the downloaded SDF file by clicking on the "choose file" option and then choosing the SDF file from the downloads folder. Finally, they emphasize carefully selecting the PDB option and 3D coordinates.