Distance monitoring...



Distance monitoring is used to compute and monitor interatomic distances. In addition to simply computing the distances (as in the measure distance command) the monitoring commands add a graphical representation for the measured distances: the pairs of atoms in the monitor list will be connected by a dotted line, labeled with the current distance between the two atoms (using display coordinates). If the monitored interatomic distances change (e.g. during energy minimization), the corresponding monitor labels will be updated dynamically. Type
Wit!P> measure monitor
monitor option: add
add monitor distance (1st atom)    [pick 1st atom or enter atom name]
add monitor distance (2nd atom)    [pick 2nd atom or enter atom name]
monitor distance /4apr/A/E/PHE_296/CE1 -- TRP_194/CZ3 = 4.803
add monitor distance (1st atom)    [pick more pairs... ]
Distances are reported in the message box, and graphically rendered by a green dotted line, labeled with the current value of the distance. Some of the graphics attribute of the the monitor lines may be changed using monitor options:
monitor option: color yellow
monitor option: width 3
monitor option: label off
to change the color of monitoring lines to yellow, increase the linewdith of monitoring lines to 3, and to suppress the display of monitoring distance labels. Note: it is not possible to change these graphics attributes for individual monitoring pairs, due to the rather primitive internal data structure used by the Wit!P graphics server to store monitoring information.

The display of monitoring lines may be suppressed entirely by

monitor option: off
Note, that you may add new monitoring pairs, even if displaying of monitoring lines is disabled. The newly added (and all other) monitoring lines will become visible again, once you enter
monitor option: on
To clear the distance monitor pair list type
monitor option: clear
Again, it is currently not possible to remove individual monitoring pairs from the list.

When analyzing molecular structures, one is frequently interested in short distances between groups of atoms (e.g. the enzyme and a ligand). It would be extremely tedious to set up a complete list of monitoring pairs corresponding to all short distances. Fortunately, one of the monitor options lets us set up the list quite painlessly. E.g:

monitor option: close 3.3 ///I -done ///E -done
would augment the monitor pair list with all pairs with first atom in ///I (inhibitor, "from"-atoms) and second atom in ///E (enzyme, "to"-atoms) for which the current distance (using display coordinates) is less than 3.3 A. The same monitor option may be used to find short intramolecular distances:
monitor option: close 3.3 ///E -done ///E -done
Since one is usually not interested in close contacts between bonded atoms (directly, or 1-3 and 1-4) the monitor close command does not add such "uninteresting" pairs.

The monitor vdw command is very similar to monitor close, but here the distance threshold is given as a fraction of the sum of the vdW radii of the two atoms, rather than as an absolute value in A. Clear the current monitor list, and enter the following command:

monitor option: vdw 0.85 ///E -done ///E -done
Aha! This is interesting: the vdw command lists three short vdW contacts (the list in the message box shows 6 lines, but the list is redundant) all involving the OXT atom of residue GLU_325. Obviously, there is a bond missing OXT and C of this residue. You will learn how to fix such problems in a later section.

The hbonds command is supposed to add all hydrogen bonds between "from"-atoms and "to"-atoms. Sadly, the command is rather difficult to use and works only under some stringent assumptions (all polar hydrogens must be present, H-bond donor and acceptor attributes of atoms must have been set correctly):

monitor option: hbonds 2.5 ///E -done ///I -done
would add monitor pairs between H connected to donor atoms and acceptor atoms, one atom from the enzyme, the other from the inhibitor, provided that the H -- donor distance does not exceed 2.5 A.

A different way to set up H-bond monitor pair lists, which works without the need for the presence of polar hydrogens, is to use the close option:

monitor option: close 3.3 ///E -atom symbol N,O -done -done
[0 atoms selected] monitor close contacts to atoms: ///I -atom symbol N,O -done -done
(for a list of intermolecular enzyme/inhibitor H-bonds).

There is one more monitor command that sets up a whole list of monitoring pairs: autopairs, which is closely related to automatic molecular superposition, and will be discussed in the corresponding section of this tutorial.

And finally, there are some options which control the textual output of the monitor command:

monitor option: list file monitor.txt
which will cause textual output to go to the file monitor.txt, rather than the message box. To close the file, and switch back to textual output into the message box enter
monitor option: list terminal
suppress textual output by
monitor option: list off

The next section is about using move and copy to manipulate the molecular data tree.



A.Widmer, NIBR/CPC/CSG-SB