The command to read in a PDB file is (surprise, surprise...)
Wit!P> read pdb /db/pdb/4aprSo, go ahead, and either enter the command through the keyboard, or else pick Read from the menu (remember: right-click to pick, if you are using the default mouse settings), followed by pdb, then enter the filename /db/pdb/4apr in the command line of the command/message box. Note that the read pdb command assumes a default extension ("file type") of .pdb, a feature which allowed you to use a slightly abbreviated form of the filename.
The program responds by displaying a number of messages in the command/message box:
Only the last 5 lines are visible in the message box, but you may use the cursor keys of the keyboard to "scroll" the message box (Shift-CurUp/Shift-CurDown) or to expand and shrink the size of the message box (Alt-CurUp/Alt-CurDown), or hit Shift-F1 to expand the message box to take up the entire space of the 3D window. Hit Shift-F1 again to shrink the message box to its previous size. (Consult the sections on Keyboard Shortcuts and on Function Keys for a complete list of keyboard shortcuts).reading molecule from file /db/pdb/4apr ... HEADER HYDROLASE (ACID PROTEINASE) 03-AUG-89 4APR 4APR 2 COMPND ACID PROTEINASE (RHIZOPUSPEPSIN) (E.C.3.4.23.6) COMPLEX 4APR 3 COMPND 2 WITH A PEPSTATIN-LIKE RENIN INHIBITOR 4APR 4 SOURCE BREAD MOLD (RHIZOPUS $CHINENSIS) 4APR 5 AUTHOR K.SUGUNA,D.R.DAVIES 4APR 6 CRYST1 60.390 60.610 106.900 90.00 90.00 90.00 P 21 21 21 4 4APR 236 2762 atoms read from /db/pdb/4apr
So, now we know that program has read 2762 atoms from /db/pdb/4apr.pdb. We can't see the molecule, because the 3D window id displaying only a finite extent of the entire 3D coordinate space (approx. += 10 Å) around the origin (0,0,0) and none of the atoms in the file 4apr.pdb has coordinates that falls within this visible part of the world.
The following command will "find" the molecule for you:
Wit!P> display find / /4aprIf you are entering the command through the menu, make sure that you pick "/", not "/4apr", when prompted for the "object" to find, and that you end the command by picking done from the menu. The display find command will translate the "root" object ("/" = all molecules) such that the center (average coordinate) of all atoms in the molecule 4apr is shifted to the center of the visible part of the world.
Now that you have found the molecule, it's time to play with it...