Models
There are two models offered:
Preset range | corresponds to the drawings given in the Atlas of
Zeolite Framework Types |
User-defined range | initially this is just a little more than a unit cell; the
range can then be specified in fractions of the cell parameters |
Manipulation of the structure
To manipulate the orientation of the structure, place the cursor on the drawing, and use one of the following combinations:
to rotate around the vertical axis |
press left mouse button |
move the mouse left / right |
to rotate around the horizontal axis |
press left mouse button |
move the mouse up / down |
to rotate around the axis ⊥ to screen |
press Shift + left mouse button |
move the mouse left /right |
to zoom in / out |
press Shift + left mouse button |
move the mouse up /down |
use scroll wheel |
|
Display options
The framework can be displayed with just the Si atoms or with both Si and O atoms
shown. There are several different display styles to choose from: wireframe, stick, ball and stick,
or ionic radii (1.4 Å for O atoms). Three stick widths are available.
Note: All models are idealized framework models in the highest possible symmetry
Four types of surfaces can be calculated and displayed (solid, transluscent, mesh
or dots):
(1) |
cages: defines closed cages, normally not accessible to sorbed molecules |
(2) |
channel system: defines the internal surface that is accessible to a sorbed molecule
(see notes below) |
(3) |
two-sided channel system: different colors are used for the inner and outer sides of
the channel surface. The two sided display works best for wider channels. The surface option
radio buttons apply to the inner surface. Try using "mesh" with this option. To change the
outer surface see Advanced Users below. |
(4) |
framework wrap: approximate "van der Waals" envelope of the framework. This surface
is calculated around the oxygen atoms (radius 1.4 Å) by "rolling" a sphere with radius
1.4 Å around the framework. |
Resolution
|
For the channel systems there are three options for the surface resolution. The higher
the resolution, the more detailed the features of the surfaces. After changing the resolution,
you must clear the current surface (select "no surface") and then select the type of surface
desired. |
Note:
(i) |
The calculation of the surfaces is done locally and can take time. The time depends on
the size of the model and on the power of your computer - be patient. The status bar at the
bottom of your browser will indicate if a calculation is in progress (script started) or
finished (jmol script terminated). |
(ii) |
You can use the "hide all atoms and bonds" button to display just the channel surfaces
and/or cages. |
(iii) |
When generating many different surfaces, the Java Applet might hang. Just reload the
page. If this fails, restart the browser. |
Change the color of surfaces, atoms or background
Colors may look different on different screens or when printed. You have full control over all colors either by typing in a command in the textbox under "Change colors" or in the "
Jmol Console" (see
Advanced Users).
Syntax:
for surfaces:
color $surfacename colorcode
where
surfacename = cage or channel or outer or inner or wrap
Example
to change the inner surface of the two sided channel display to "limegreen":
color $inner limegreen
for atoms:
select atomtype; color atoms colorcode
where
atomtype = silicon or oxygen
Note: the bonds "inherit" the color of the atoms
Example
to change the silicon atoms to "darkorange":
select silicon; color atoms darkorange
for background:
color background colorcode
Example
to change to white background:
color background white
colorcode:
The color can be specified in 3 different ways:
- as a JavsScript
color name (as in the example above)
- in hex notation as [x32CD32}, see
examples
- in rbg notation as [50,205,50]
Advanced Users
Click on the
Jmol "logo" (bottom right) or the right mouse button for further
options.
These include: defined viewing directions, changing the color of the atoms, distance measurements, etc.
Open "Console" in
Jmol menu and type any
Jmol command to modify the drawing. See the
documentation on
Jmol
commands.
Please report any problems/suggestions regarding this tool to Christian Baerlocher (
christian.baerlocher@mat.ethz.ch)
last updated: 14-April-2025