Appion

From Dmitry:

I ran makegoodaverages.py today, and it ran fine for me.

I looked at the command that was issued in (/ami/data00/appion/
10sep01b/recon/emanrecon4/eulers/refine4_10oct14o45) and noticed that
--avgjump=0. What that means is that the program will not process any
particles, since it's virtually impossible to come across a particle
whose Euler angles stay exactly the same from iteration to iteration.

The webpage defaults to setting this value as 0. What we can do is
remove the issuing of a default value, so that the user has to make
sure to set it, and issue a warning on the following page if this
value is 0. Additionally, we can look at the python and make sure that
it doesn't fail if 'nprtcls<1' or provides adequate documentation on
the issue.

Thanks for the update. Do you think we could chose a "smart" default value that would work well for newbies who don't know what they are doing?
I think we are missing documentation on this feature so far.

Yes, we can choose a "smart" value. A good initial guess would be the average median Euler jump. This is reported in the reconsummary.php page. The full statistics on the Euler jumpers are in eulergraph.php. See, for example, http://cronus3.scripps.edu/~dlyumkis/myamiweb/processing/reconsummary.php?expId=1680, and look at the last two reconstructions, where the average jumps are 22.3 and 17.0, respectively. We can set the value in the makegoodaverages.php page to the median value for the corresponding reconstruction. It might not be a bad idea to add checks / documentation to the python code though, if this error comes up again.

There is some explanation for this value in the pop-up menu, but you're right, we don't have full documentation on it.