5.2 PLUTO Worked Examples
This example uses the data for ABBUMO10, which had been selected as a hit
during a QUEST search, and is the first item in the probname.dat file. The
first display will be the default style of stick drawing with element colour
- Select Sol this draws atoms with standard radii.
- Select Shad this adds shadow lines.
- Select Atm- this decreases the atoms sizes, try also Atm+, and Adef.
- Select Bon- this decreases the bond thickness, try also Bon+.
Example 1: Solid atom view of ABBUMO10
Then try out rotation and moving to other entries:
- Select Sol this toggles back to stick style.
- Select < > ^ v this causes rotation of the image in steps of 3
- Select Rset this resets the display to the starting options and view.
- Select Next to move to the next data entry.
- Select Prev to move to previous entry.
Example 2: Stick view of ABBUMO10 with distance, angle and
Staying with the previous data entry ABBUMO10, try the following :
- Select atom click on an atom to display the atom label.
- Select Labl to display all labels, and select Nola to switch off labels.
- Select Hydr this toggles hydrogen display on/off.
- Select Dist then click on two atoms to display the distance.
- Select Angl then click on 3 atoms to display the angle.
- Select Tors then click on 4 atoms to display the torsion angle
- Select Nodi to switch off display of distances and angles.
- Select Rset for standard view of ABBUMO10.
- Select Sol then select Shad and VdW for van der Waals radii (see 3(a)).
- Select Sol to toggle back to stick diagram.
- Select Cell to display unit cell. This may be toggled on/off.
- Select Vy to plot view projected down b-axis of cell.
- Select Pack to plot all molecules within the unit cell.
- Select +c/2 to add molecules by extending range by +c/2 (see 3(b)).
- Select Sol to turn on solid style, which is still van der Waals radii (see
Example 3(a): Space filling view of ABBUMO10.
Example 3(b): Packing diagram of ABBUMO10, viewed down b axis.
Example 3(c): Packing diagram with van der Waals radii
- Select Rset to reset to standard view of ABBUMO10.
- Select Hydr to switch off hydrogen display.
- Select Hbond and select again twice for default distance limits
(sum of van der Waals radii of H and acceptor atom - 0.2Å). This displays all H-bond contacts shorter than these limits for N and O donors and acceptors. Note that the two H-bonds of
2.038Å are symmetry related.
- Select Strt to start the expansion of a network of H-bonds.
- Select Exp which asks you to click on a link atom (numbered in blue).
- Select link atom 1 to add the molecule at link atom 1 (link atoms are re-numbered).
- Select Exp
- Select link atom 3 to add the molecule at link atom 1.
- Select Exp
- Select link atom 3 to add the molecule at link atom 3.
- Rotate ad lib.
- Select Cell to show molecules form a chain along a 21 screw axis
parallel to b.
- Select Nbo+ to display non-bonded contacts thicker. Try also
Example 4: Expanded network of H-bonds (ABBUMO10)