Home
Preferences

Preferences are employed to configure jems. Preferences are organized in several tabs:

The toolbar contains tool buttons to:

Top
Atom colors

Figure1

Figure 1 Atom color selection.

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.

Top
GUI colors

Figure2

Figure 2 Color selection.

This tab sets some of the colors used by jems plots and panels. To change one of these, click on the colored button.

Top
Contour plot

Figure3

Figure 3 Contour plot parameters.

This tab sets the number of contour levels as well as the contours color.

Top
Debug options

Figure4

Figure 4 Debug options.

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.

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.

Top
Display

Figure5

Figure 5 Display options.

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
Font

Figure6

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
Imaging

Figure7a

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.

Figure7b

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
Indexing

Figure8

Figure 8 Indexing options.

Sets the default pixel size of the experimental images (here CCD camera with 24 μm pixels).

Top
Mail

Figure9

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
Measurement

Figure10

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

Top
Microscope

Figure11

Figure 11 Microscope selection.

Set the default microscope and the range of the CTF:

Top
Miscellany and default crystal

Figure12

Figure 12 Miscellany and default crystal selection.

Top
Noise type

Figure13

Figure 13 Noise type and amplitude.

Top
Look and Feel

Figure14

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
Image format

Figure15

Figure 15 Format of saved images.

Top
Java VM

Figure16

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:

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
Help URLs

The URLs to access jems help files on http://www.jems-swiss.ch are defined as (Fig. 17):

Figure17

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.

Figure18

Figure 18 Localhost Help URLs.

The whole jems-swiss help file system can be downloaded (jemsHelpFiles.zip). It has to be installed as a website even on the localhost.