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How to run manual picking and mask making » History » Version 1

Amber Herold, 10/12/2010 02:27 PM

1 1 Amber Herold 
h1. How to run manual picking and mask making
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Manual picking and mask making use GUIs and require user interaction. 





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When running these at AMI, you can use amibox02 or amibox03.





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When you ssh, you need to use the -X flag to tell the terminal to display the GUI.





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<pre>





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ssh -X amibox02





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</pre>





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Then put the correct path to appion in front of the command, such as /ami/sw/bin/appion.





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<pre>





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/ami/sw/bin/appion makestack2.py --single=start.hed --selectionid=1002 --invert --normalized --maskassess=manualrun1 --boxsize=16 --description="test" --projectid=5 --preset=upload --session=10may13l35 --runname=stack7 --rundir=/ami/data00/appion/10may13l35/stacks/stack7 --no-rejects --no-wait --commit --reverse --limit=1 --continue





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</pre>