FAQ

From OpenChrom-Wiki
Jump to: navigation, search

Contents

General

Do I need to create a user account in order to use OpenChrom?

When you download and install OpenChrom for the first time, you can use OpenChrom for 30 days without needing to create a user account. After the trial period of 30 days the use of the OpenChrom Community Edition remains free, but a registration (minimum: user name and email) is necessary. The registration is done via the website http://www.openchrom.net.

Do I need any serial keys?

In order to utilize all plug-ins (e.g. data converters) after the trial period of 30 days, for most plug-ins the generation of a serial key will be necessary. You can generate and retrieve the serial keys for each plug-in on the "marketplace" which you can access via the website http://www.openchrom.net (Software|Plugin). Note, that you are required to create and log into a user account.

How to cite OpenChrom in scientific papers?

Use the following references to cite OpenChrom:

  • OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data, BMC Bioinformatics, 2010, http://dx.doi.org/10.1186/1471-2105-11-405
  • Post-optimization of Py-GC/MS data: a case study using a new digital chemical noise reduction filter (NOISERA) to enhance the data quality utilizing OpenChrom mass spectrometric software, Journal of Analytical and Applied Pyrolysis, 2011, http://dx.doi.org/10.1016/j.jaap.2011.05.013
  • Characterizing odorous emissions using new software for identifying peaks in chemometric models of gas chromatography – mass spectrometry datasets, Chemometrics and Intelligent Laboratory Systems, 2012, http://dx.doi.org/10.1016/j.chemolab.2012.07.006




Marketplace / Website

Where can I create a free account?

You can register yourself here (https://marketplace.openchrom.net/register).

Does the account cost anything?

No, it is free. You can skip your account at any time.

Where can I log-in myself?

You are able to log-in yourself here (https://marketplace.openchrom.net/login).

I forgot my password. Can I reset it?

Yes, you can (https://marketplace.openchrom.net/password).

Where can the serial keys for the proprietary plug-ins be retrieved?

After you've been logged in, there is a function to create a serial key on each proprietary plug-in page, e.g. (https://marketplace.openchrom.net/plugin/Agilent+FID+Import+Converter#plg_get_key).


OpenChrom - Installation

Can the latest version of OpenChrom (0.9.0) run on an older version of Mac OS X (10.6 and older)?

Yes, if a copy of OpenJDK 7 can be installed.

Can an OLDER version of OpenChrom run on ANY version of Mac OS X with just the Apple provided Java SE?

Yes and no.

Intel Macs running 10.5.8 and later

Intel Macs running 10.5.8 and later should have installed the 64-bit version Java SE 6 and should be able to run OpenChrom 0.5.0 without the need of installing any addition software. PPC Macs running up to 10.5.8 and Intel Macs running 10.4 only have the 32-bit version of Java SE 5 installed. OpenChrom 0.5.0 and older appears to require a minimum of Java 6. (It would have been nice if this additional requirement was documented somewhere.)

Are pre-compiled binaries for OpenJDK 7 available?

Yes, for Snow Leopard (10.6) and Lion (10.7). For Leopard (10.5), maybe.


Working with OpenChrom

I can not open my chromatogram data file, although OpenChrom claims to give access to several vendor formats!

Most data converters are not bundled together with the OpenChrom Community Edition and have to be installed afterwards. They are still free to use. Please have a look here.

How do I display several chromatograms in overlay mode?

Please have a look here.

I can not distinguish between my overlayed chromatograms. Can I change the color scheme of the overlayed chromatograms?

Please have a look here.

Known Issues

I downloaded the zipped Windows installation package of OpenChrom, but when I try to start the installation by unzipping the files the process is stopped!

Instead of using the default Windows unzipper, we recommend to use the free and open source file archiver 7-zip to unzip the software. The default Windows archiver fails, because it is limited to a certain length of characters.

I installed OpenChrom and wanted to fetch plug-ins from the Marketplace, but the Marketplace won't open!

If your computer happens to be located behind a proxy server (frequently the case in companies and universities) you, ask the responsible IT-service for the necessary proxy settings and follow the instructions under OpenChrom behind a proxy. After correct proxy settings have been set, you will most likely be able to reach the Marketplace.

OpenChrom is unable to start!

Your computer may not have enough RAM or the default OpenChrom settings for memory allocation ("heap settings") may not be optimal for your computer.
Solution: The heap settings are located in the openchrom.ini file, which you find in the OpenChrom folder. Open openchrom.ini with a text editor and try to solve one of the above issues by changing the initial ("Xms") and maximum heap size ("Xmx"): e.g. -Xms512M to -Xms256M and -Xmx2048M to -Xmx1024M. The maximum heap size should be at least 2 times bigger than the initial heap size. Don't forget to save the changes before closing.

Loading of data files takes unusually long or is stopped!

The data file might be unusually large (e.g. MALDI-TOF files). So far OpenChrom is not optimized for very large data files (e.g. 1 GB or larger). Or your computer may not have enough RAM or the default OpenChrom settings for memory allocation ("heap settings") may not be optimal for your computer.
Solution: The heap settings are located in the openchrom.ini file, which you find in the OpenChrom folder. Open openchrom.ini with a text editor and try to solve one of the above issues by changing the initial ("Xms") and maximum heap size ("Xmx"): e.g. -Xms512M to -Xms256M and -Xmx2048M to -Xmx1024M. The maximum heap size should be at least 2 times bigger than the initial heap size. Don't forget to save the changes before closing.

I have opened multiple data files, but I can not open any further data file!

Your computer may not have enough RAM or the default OpenChrom settings for memory allocation ("heap settings") may not be optimal for your computer.
Solution: The heap settings are located in the openchrom.ini file, which you find in the OpenChrom folder. Open openchrom.ini with a text editor and try to solve one of the above issues by changing the initial ("Xms") and maximum heap size ("Xmx"): e.g. -Xms512M to -Xms256M and -Xmx2048M to -Xmx1024M. The maximum heap size should be at least 2 times bigger than the initial heap size. Don't forget to save the changes before closing.

I downloaded openchrom_macosx.cocoa.x86_0.6.0.zip and it does not work!

The reason why this binary does not work is that it requires a 32-bit version (Intel) of OpenJDK 7 and not the 64-bit version. If someone could build a 32-bit version of OpenJDK 7, then someone might even be able to run OpenChrom 0.6.0 on an Intel Mac running an OS as old asTiger 10.4!

I downloaded openchrom_macosx.cocoa.ppc_0.6.0.zip and it does not work!

That reason why this binary does not work is that it requires a PPC version of OpenJDK 7. If someone could build a PPC version of OpenJDK 7, then a person could run OpenChrom 0.6.0 on any PPC Mac!

Has anyone been able to use either macosx.cocoa.x86_0.5.0.zip or openchrom_macosx.cocoa.ppc_0.5.0.zip?

I doubt that there exist a single person that has been successful in using either Mac version of OpenChrom since both versions requires Java 6, which Apple had not provided and the few OpenJDK 6 or 7 binaries available appear not to work. It would have be nice if these facts were included in a README file to avoid unnecessary downloads.

While starting OpenChrom, I receive an error message starting with: "Java was started but returned exit code=13"

It is most likely because of an incompatible Java version being installed on your system, i.e. if you have installed the OpenChrom 64-bit version it demands a 64-bit Java version. Please double-check by opening the command line interface of your system and type: java -version
If you have a 32-bit java version installed please update to a 64-bit version.

While starting OpenChrom, I receive an error message starting with: "Java was started but returned exit code=1"

It is most likely because of too high RAM settings in your local "openchrom.ini" file, which you find in the OpenChrom installation folder. Open openchrom.ini with a text editor and change the initial ("Xms") and maximum heap size ("Xmx"): e.g. -Xms512M to -Xms256M and -Xmx2048M to -Xmx1024M. The maximum heap size should be at least 2 times bigger than the initial heap size. Don't forget to save the changes before closing.