Leginon

Hi Venkata,

Unfortunately it seems as this is not yet supported - a fast workaround is to create templates from the ML2D result, run a spider reference based alignment and then use the results of this clustering run for the common lines.
(this is what I would do anyways - in my experience this works best).
If you are desperate and really want to run common lines on the obtained classaverages you can always leave appion and upload the resulting model back into the database using the upload initial model function. You can find the averages at the path that is displayed in the Alignment Stack List window under stack file: ....

Let me know if that worked and if you need more help,

Best,
Arne

Hi Arne,

I have done exactly as you said and the results are better. But still my problem of selecting the class averages from ML2D or Spider reference based alignment, in the top down menu of EMAN common linesinterface doesnot show it.

Anyhow I started to do clustering using SPIDER Caron(though I donot need it) only to make them availble in EMAN common lines interface. I encountered this error during the run of SPIDER caron.

waiting for spider........................................
SPIDER completed in 1 hr 51 min SPIDER NORMAL STOP
Traceback (most recent call last):
File "/usr/local/bin/coranClassify.py", line 196, in ?
coranClass.start()
File "/usr/local/bin/coranClassify.py", line 171, in start
numpart=numpart, numfactors=self.params['numfactors'])
File "/usr/lib/python2.4/site-packages/appionlib/apSpider/classification.py", line 82, in correspondenceAnalysis
contriblist = analyzeEigenFactors(alignedstack, rundir, numpart, numfactors, dataext)
File "/usr/lib/python2.4/site-packages/appionlib/apSpider/classification.py", line 115, in analyzeEigenFactors
apDisplay.printError("Failed to create Eigen images")
File "/usr/lib/python2.4/site-packages/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
Failed to create Eigen images

thanks,

regards,
venkata

Hi Venkata,

I was not able to reproduce the error you got with my data.
On my end common lines are running fine.
Try to rerun the Coran classification with a binning factor of 2 - maybe this can resolve it.
I will try to figure out whats going on.

Did you click on the class averages to do the common lines or did you used the common lines directly from the side bar?

If the latter is the case try to select the classaverages you want to be used for the common lines and then hit the run common lines button with those averages selected.

Arne

Hi Arne,

sorry for late relply, I did not go through all the options in the class averages webpage. I found it just a day before I received your message and so I already tried it. It worked well.

Thanks for the support.

regards,
venkata