Reading a molecule from a PDB file



Read in the file 4apr.pdb from the PDB database, which is located in the directory  /db/pdb (the location of the PDB files may be different at your site. If you don't know where to find PDB files, right-click here, and save a copy of 4apr to the directory from which you started Wit!P).

The command to read in a PDB file is (surprise, surprise...)

Wit!P> read pdb /db/pdb/4apr
So, 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:

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
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).

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 / /4apr
If 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...



A.Widmer, NIBR/CPC/CSG-SB