Either implement the function needed to modify local alignments from IMOD or add something to automatically ignore those files as they seem to be creating problems from some users.
While looking at this, confirm this is working appropriately when tilts are specified as ignored in autoAlign. I think in that case, they should not need to be re-specified in ctf estimate, however, in my current project, I've seen hints this may not be working.
Either implement the function needed to modify local alignments from IMOD or add something to automatically ignore those files as they seem to be creating problems from some users.
While looking at this, confirm this is working appropriately when tilts are specified as ignored in autoAlign. I think in that case, they should not need to be re-specified in ctf estimate, however, in my current project, I've seen hints this may not be working.