Appion

Sorry. Uncommented in r18439. I meant to undo that before committing.

Ramp normalization screwed up my data in the past. If you have a particle near the carbon or some other dense structure (gold fiducials) the ramp with be too steep and it will really screw up your particle. The Asturias lab (or at least Ed Brignole) stopped using it for this reason.

Something was wrong with the code, so I could NOT turn it off. Even when I removed the xmipp normalize it was still running xmipp normalize. The only was I could fix it was to comment out the code.

Second, we should not need to use Xmipp for this task it really simple code that was implemented in appion, before we started using Xmipp, see teh planeRegression() in appion/appionlib/apImage/imagefilter.py

Sorry again. I went through the code change again and that should have been the only change that would affect the data. Other than how you select the best CTF parameters.

You are going to need to have Sargis or JC update garibaldi as well.

thanks for fixing this. This doesn't involve any changes to the python code, so garibaldi should be fine. myamiweb should be updated on the web servers though.