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Why does alignSubStack.py need include/exclude class list? #496

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 496, https://emg.nysbc.org/redmine/issues/496 Original Date: 2010-05-17 Original Assignee: Pick-Wei Lau

It makes no sense to me. Particle alignment does not put particles into classes. Why does the script and its webpage insist on inputting at least one of the two?

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2010-05-18T02:37:14Z

Also, even with clustered particles, if I select all classes, it won't let me create a substack. viewstack.php button for creating substack does not function in this case. Why not? I want to use the linked substack with the alignment information for subtomogram averaging.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2010-05-19T19:29:09Z

Particle alignment DOES put particles into classes. Without defining a exclude or include list you are including ALL particles which not really a substack. The max shift and max score/spread function were added later.

If max shift and max score/spread are not defined then exclude and include are not required. Otherwise they have to be there. We will need to check both the python and php code for this.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2010-05-19T19:58:12Z

O.K., I will use all particles to generate the reference classes and then use them as fake include classes to make my special substack, then. How about just fix the deactivated button in stackviewer to allow selection of all classes?