View molecule orbiltals, total densities and conolly surfaces

1. Go to Plot - Contour. A "Contour Control"-window pops up.
2. Click Browse to find your .plt-file.
3. Select your file and click Open.
4. Click Import file.
5. In the "Define contour levels"-boxes, give
   1. a minimum and a maximum value and choose a colour by clicking the Colour(#)-button, if you are viewing molecule orbitals. Next to Mapping-button is given the name of the orbital file and next to that the minimum and maximum values of the orbitals.
   2. a value for the total electron density, if you are viewing the total electron density. The values in between which this value must fall are given next to the file name, which is next to the Mapping-button.
6. Click Apply.
7. You should see the orbitals or the total density in the "3D"-window. If not, adjust the values and click Apply.

Display Cut planes

1. Import a Contour-file the way you did in the previous step but do not display it and click Dismiss.
2. Go to Plot - Cut Plane. A "Contour Plane Control"-window pops up.
3. Mark one of the planes and click Apply. You should see the plane. You may have to zoom out a bit to see the whole plane.
4. To view another plane, unselect the plane you selected last time and pick another plane and click Apply. You can view two planes at the same time if you want to.

• For more information in viewing the electron densities and cut planes, please refer to the tutorials or the manual.

View Conolly surfaces and electron density on the molecule surface

Electron density on the molecule surface
1. Read in your molecule structure from File - Import coords
2. Convert the total electron density of your molecule to a .plt-file.
3. Go to Run - Pltfile (conversion)
4. Read in your electron density .plt as input-file.
5. Give the output file a name which ends .txt.
6. Mark "Unformatted = => Formatted"
7. Click Apply.
8. Write down the min. and max. values for X, Y and Z with at least four decimals. Write down the values for Xpoints, Ypoints and Zpoints as well.
9. Click Dismiss
10. Go to File - Export - Input - Probesurf.
11. Give the name of your input file (.inp) in the "File name"-box.
12. Write in the boxes the X, Y and Z min and max values as well as the values for X, Y and Z points. You can leave the "Probe radius" at its default value.
13. Click Apply and then Dismiss.
14. Go to Run - Probesurf (Conolly)
15. Give your .inp as input file. Go through Browse to find it.
16. Give the output file a name, which ends .plt. Note that you do not give the same name as to your total density file!
17. Click Apply.
18. To the question "Do you want to read in a conolly surface" answer "Yes" and the surface will be read in automatically.
19. Click Dismiss in the "Probesurf"-window.
20. Read in your total density file in the "Contour Control"-window as before.
21. Map the total density to conolly surface by clicking Mapping next to conolly surface file name and from the list, choose the total density.
22. Give no value for total density.
23. Mark conolly surface
24. Write in the first box the percentage you want to have for the conolly surface and after that the min. and max. values for the total density. Separate the different values with spaces.
25. Click Apply.
26. You might have to adjust the values to be able to see the electron density of the molecule surface.