Start ADFinput Go to the Protein panel (for example, by choosing the 'Protein' command from the Model menu) Click on the 'Select' button Use the file select box to open the 1BXU.pdb file (in the $ADFHOME/examples/PDB directory)
In the main window the protein will be displayed. Note that this particular PDB file contains some water molecules, they are also shown. Next select one of the residues:
Click somewhere on the backbone (the ribbon showing)
You should have an image that looks similar to this:
You will notice two pull-down menus: one to select how to visualize the backbone (currently 'Ribbon'), and one to select how to visualize the sidechains (currently 'None'). Use these to examine the different visualization options:
Select 'CA' to show only the C-alpha atoms from the backbone Select 'Show' to show the sidechains Rotate and zoom as usual ...
You can select residues by clicking on the backbone. Alternatively, you can select one or more residues (or other atoms contained in the PDB) by selecting them in the list. Use the modifier keys to extend the selection, or to remove items from the list of selected items:
Select a number of residues by shift-clicking in the list of residues Remove one of the selected residues by control-click in the list
For the tutorial, we will use the default visualization setup:
Hide de sidechains Show the backbone as ribbon again
