Re: [Mzmine-devel] Bug report: No 3D plots

2010-11-01 Thread Pudney Chris (ext) GBJH
G'day, > However when I load mass spectral data and click on “Visualisation / 3D > plot nothing happens. The 2D and TIC plots all work fine. You can also explicitly check whether Java3D has been installed by visiting your JRE's installation home directory, e.g. C:\Program Files\Java\jre6 and th

Re: [Mzmine-devel] Bug report: No 3D plots

2010-11-01 Thread Tomas Pluskal
Hi Mark, Somehow your Java runtime and Java3D library are not linked properly. Did you install 64-bit version of Java as well as 64-bit version of Java3D? Can you run these 2 commands on the windows command line and let me know the output? 1) java -version 2) java -d64 -version Also, you can

[Mzmine-devel] Bug report: No 3D plots

2010-11-01 Thread mark.earll
Hi Tomas, I have installed mzmine 2.1 on windows 7 64 bit with Java 6 and Java 3D installed. I have verified that Java 3D works by visiting the java 3d test page at .downloadjava3d.com/java3dtest.php and indeed I do see a 3D spinning image. (The hardware is an Intel Xeon 8 core processor wi

Re: [Mzmine-devel] questions about normalization

2010-11-01 Thread Tomas Pluskal
Hi, Values less than 1 are not so easy to read, so the module adjust the final values linearly so that the maximum intensity is equal to 10. That makes the intensities more human-readable. You can check the source code for details: http://mzmine.svn.sourceforge.net/viewvc/mzmine/trunk/src/

[Mzmine-devel] questions about normalization

2010-11-01 Thread toms
Hi, I have some trouble in understanding the "linear normalizer/total raw signal". According to the MZmine 2.0 manual, the normalization by "total raw signal" should follow the formula: normalized peak signal=(a peak signal of a sample)/ (the total signal of the same sample), that is, the resul