The toolbar contains tool buttons to:
This tab changes the atoms color. The atom color is used by perspective plots and by the atomic column cursor.
Click on the colored button.
This tab sets some of the colors used by jems plots and panels. To change one of these, click on the colored button.
This tab sets the number of contour levels as well as the contours color.
The debug options pane allows to display more information in the console or in system output stream.
They help to figure out when a bug occurs.
- Blochwave: print and/or display the secular matrices and related vectors.
- CIF: display status when loading of CIF files is difficult.
- Debug (simple): output simple debug information like javaVM configuration, paths to system files, etc.
- Debug (extended): output metrics, space-group, atomic scattering amplitude.
- Finalize: tracks java VM memory leaks.
- Fit: Levenberg-Marquardt fitting info.
- Format prints formatting info.
- Graphics: tracks graphics objects.
- HAADF: HAADF info.
- Imaging: tracks imaging objects.
- Indexing: tracks SAED indexing objects.
- Keyboard: tracks keyboard events.
- License: tracks license settings.
- Memory: enables a change of java VM initial and maximum sizes.
- Mouse: tracks mouse events.
- Multislice: shows more of the multislice generated images and data.
- Printing: tracks printing of images and graphics.
- Processing: images processing info.
- Space-group: shows the full space-group info.
- Table: tables info.
- Thread: thread running and info.
- Timing: timing info.
- Variant: variant diffraction info.
- Window state: tracks window open, close, activate.
- Zone axis: shows zone axis geometry and related parameters.
This tab also allows to set the number of CPUs and the class of objects tracked by the finalizer.
Note that computer intensive calculations should be done with the VM multi-threading checkbox checked. The optimum
number of cpus should be tested. A too small number will make calculation last longer. A too large number can have
the same effect.
This tab sets options employed for displaying powder lines and 3-D structures. Depending on the number of
atoms and the volume of the unit cell the 3-D perspective plots are drawn with more or less
color levels in order to speed up the display.
Top

Figure 6 Sets Font size and type.
Font type and size selection. Be careful not to set an unavailable font. In case of trouble the font is specified in
file jemsPreferences.txt in the default jems folder created in the user home directory.
Top

Figure 7a Imaging dimensions.
Set the maximum dimension of Graphical User Interface panels. For law resolution
screen, 128 pixels, it should be set to 512. Set the dimension of images when reduced. Set the maximum dimension of
calculated images and maps of images.
The projected potential of the crystal must sampled when performing multislice calculations. A typical value
is 0.010 which samples the potential with a maximum sampling interval of 0.010 nm, i.e. 0.1 Å.

Figure 7b Imaging options.
Set minimum amplitude of the reflections that participate to the HRTEM images. When making image maps each stripe
is displayed. Set the maximum order of the Aberrations that will appear in the GUI. Resite images when
loading images of dimension larger than the maximum dimension. When calculating potential by the Direct method
set interpolation technique. Power spectrum are displayed either using a linear or logarithm scale. When using a log
scale scale multiply the image pixels value by a number. Set the default source of the Atomic
Form Factors. Enables java3D GUI. Set the sign of underfocus of the (CTF). Enables Holography simulations. Check site occupancy(when defining new structures),
it should be maximum 1.0.
Top

Figure 8 Indexing options.
Sets the default pixel size of the experimental images (here CCD camera with 24 μm pixels).
Top

Figure 9 Mail settings.
The Mail settings depend on the local mail server. Ask your system manager in
case of problems. The Enable mail checkbox allows to automatically send newly defined
crystal structure to jems-swiss website. It also reports errors.
Two factors authentication not supported.
Top

Figure 10 Measurement options (Bloch-waves to include).
Top

Figure 11 Microscope selection.
Set the default microscope and the range of the CTF:
- 0 to 10 for transfer down to 10 nm-1 (or 1 angstrom).
- 0 to 20 for transfer down to 20 nm-1 (or 0.5 angstrom).
Top
Miscellany and default crystal

Figure 12 Miscellany and default crystal selection.
Top

Figure 13 Noise type and amplitude.
Top

Figure 14 OS Look and Feel selection, events tracking.
The Look and Feel setting defines the Graphical User Interface. The number of available GUIs
depends on the Operating System. You may have to experiment a little with these settings in order to
find your preferred GUI.
Top

Figure 15 Format of saved images.
Top

Figure 16 Java Virtual Machine settings.
Set the initial, maximum and stack size of the Java VM machine. A typical MacOSX script is:
#! /bin/bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" > /dev/null && pwd )"
$DIR/./jre64/bin/java -version
$DIR/./jre64/bin/java -Xms2048m -Xmx4096m -Xss32m -Djava.ext.dirs=$DIR/./jre64/lib/ext -jar $DIR/./jemsMac/jems/jar/jems.jar
The script runs the java VM with options -Xms, -Xmx and -Xss that specify:
- -Xms2028m: minimum memory size [MB] reserved for the application when starting.
- -Xmx4096m: maximum memory size [MB] reserved for the application when running.
- -Xss32m: stack size [MB].
When changing -Xss from 32MB to 16MB (as an example) a copy of the script before modification is saved as:
/Applications/jemsMacOSX.app/Contents/Resources/script_2048MB_4096MB_32MB
Top
The URLs to access jems help files on http://www.jems-swiss.ch are defined as
(Fig. 17):

Figure 17 Help URLs.
By default the Site URL and Web URL are set to:
and the help files will be opened from jems-swiss web site.
These URLs can be set to a local help system in order to get a faster display of the help files. For example on MacOSX
when the jems-swiss help system is installed locally in /Library/WebServer/Documents/ the Site URL should be
set to (Fig. 18):
Using Windows when the local help system is (for example) located on D:/jems-swiss the browser address should be
specified as:
When the help system is placed on the localhost help files are accessed even when the internet connection
is interrupted.