To make protein side chains flexible during the docking, please load the molecule in PyRx using File > Load Molecule and click on + sign next to the molecule in Navigator > Molecules panel to see the list of residues. Then using Shift or Control keys, select residues you wish to make flexible. You can click on Toggle Selection Sphares icon on the main toolbar (the last icon with pink highlights) to see selected residues in 3D Scene. Then with residues selected under Navigator > Molecules panel, right click and select AutoDock > Flexible Residues menu as shown in the image below. This creates _flex folder under Navigator > AutoDock > Macromolecules panel. Select this _flex folder in Select Molecules tab when using Vina or AutoDock Wizard and PyRx would automatically prepare and run flexible docking with Vina or AutoDock respectively. Please note that making side chains flexible works only for small proteins with fewer than 200 residues. For larger proteins with more than 200 residues, PyRx might crash to guard against a stack overflow.