Measuring...



Go to the measure menu:
Wit!P> measure
(or pick Measure in the top level menu). This will put up the menu for the measuring command, offering the following options: In this section, we will explain only the first five of these menu items. The more complex monitor command will be covered in the next section, and rmsdistance will be introduced in conjunction with the molecular superposition (fit) commands.

The coordinates option may be used to list atomic coordinates:

measure: coordinates
coordinates (atom)      [pick an atom (right-click) or enter atom name]
/4apr/A/I/PHE_4/CG at 38.4240,67.8660,104.6520, displayed at -0.6545,-5.4776,-0.8284
(Note: Atom picking works only if the pick is unique, i.e. there is only one atom inside the picking window (in the UNIX version of Wit!P marked by a small square around the cursor's hotspot).

The program responds by listing the full name of the atom, and two triples of (x,y,z) coordinates. The first triple are the atomic coordinates that have been read from the file 4apr.pdb. The second triple are the atom's display coordinates, after all the rotations and translations that have been applied to the molecule with the mouse or through display rotate/translate commands. (Terminology: the first coordinates are the real coordinates, the second are the display coordinates). Translate the molecule (press middle mouse button and move the mouse...), then pick the same atom again: you will see that the z-translation affects only x,y of the display coordinates. Type (or pick) done to go back to the measure menu when you are done with the coordinates option.

Interatomic distances may be measured by

measure: distance
distance (1st atom)     [pick 1st atom or type full atom name]
distance (2nd atom)     [pick 2nd atom name]
distance /4apr/A/I/PHE_4/CD1 -- E/ASP_79/OD1 = 4.870
Distances are reported in Angstrom and are computed based on display coordinates (the distinction between real and display coordinates is only important if the two atoms are governed by different display transformations). Pick further atom pairs to measure a few more distances. Type (or pick) done when you are done with measuring distances.

Measuring angles and torsions (dihedrals) works similarly. Pick three atoms to measure the angle at the 2nd atom, pick four atoms to measure the dihedral angle between the two planes formed the 1st,2nd,3rd and 2nd,3rd,4th atom. Angles are computed based on display coordinates and are reported in degrees. Type (or pick) done to return from angle or torsion mode to the measure menu.

The principal moments of inertia may be computed with the PMOI option of the measure menu, e.g.:

measure: pmoi ///E
principal moments of inertia = 5.0312E+06, 9.1123E+06, 1.0144E+07
to compute the moments of the enzyme. The moments are computed based on real coordinates and are reported in ascending order.

Type (or pick) done to return from the measure menu to the main command menu.


Go to the next section to learn about distance monitoring.



A.Widmer, NIBR/CPC/CSG-SB