FAQ - Frequently asked questions

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How to start CheS-Mapper?

Download version

Prerequisite: Java (Version 7) has to be installed on your computer.

The latest version of CheS-Mapper can be downloaded here.

  • ches-mapper-complete.jar (executable jar file, platform independent version): If java is installed correctly, simply double click on the jar file to start CheS-Mapper.
    If you run CheS-Mapper with larger files (> 1000 compounds), use the following command line command:
    java -Xmx2g -jar ches-mapper-complete.jar (This allows CheS-Mapper to use up to 2Giga byte main memory. By default, Java processes do not get much memory. More information on visualizing large datasets is here).
  • ches-mapper.exe (Windows executable): Save the file to your computer (e.g., to your desktop), and double click to start. You have to confirm that you trust the software before CheS-Mapper starts.

Online version

Prerequisite: Java Web Start (Version 7) has to be enabled in your browser.

The latest version of CheS-Mapper with Java Web Start can be started here.

  • Windows:
    Seeing the following error-message?: Your security settings have blocked a self-signed application from running. Since Java update (version 7 update 51), the Java security settings for self-signed applications (like CheS-Mapper) are more strict. To run CheS-Mapper with Java Web Start (it is safe!), you have to lower the security settings to medium.
  • Linux:
    If you have OpenJDK installed (instead of the Sun/Oracle Java version), you additionally need the IcedTea plugin to run CheS-Mapper with Web Start. To install this plugin on ubuntu use the following command: sudo apt-get install icedtea-7-plugin. With Chrome, you have to download the jnlp-file first (after you click on Run CheS-Mapper), then rightlick on the file and select open.


CheS-Mapper does not read my dataset file.

See here for a list of supported files: Supported Dataset Formats and Size. CheS-Mapper tries to detect the file-type according to the file extension. For example, if you are using a SMILES file as input, the file should end with '.smi'.

CheS-Mapper fails on my large dataset with "OutOfMemoryError: java heap space".

You can assign more main memory to java, moreover, for very large datasets (>4000 compounds), you could try the Big data mode. Both is described here.

The compounds overlap a lot / the screen is so crowded.

Use the "+" or "-" buttons on the bottom left of the screen, as described here: Working_with_the_3D_Viewer#Change_Compound_Size

Having any problems?

Please feel free to send a mail to ches-mapper@informatik.uni-freiburg.de.