Diff for "FAQ_EMAN_USING_33"

Differences between revisions 2 and 3

Question:

We have a bit of a problem with our refinement Some of the classsums look a bit off centered and it gets worse as I do more rounds of refinement. Our structure looks more funny as I refine further. We wonder if it's worth removing the bad classsums in the initial rounds of refinements to get the rough shape of the molecule (if yes, how?).

I started with a Gaussian sphere as initial model and used these commands:

refine 2 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=8 median phasecls 
refine 10 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=5 median phasecls
refine 14 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=3 median phasecls
refine 16 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=8 median phasecls
refine 24 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=5 median phasecls
refine 32 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls
refine 42 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls
refine 44 mask=25 pad=128 hard=25 ang=6 classkeep=1 classiter=8 shrink=8 median phasecls

Answer: (Dave, Nov 20th 2007) - This has happened to me before - try generating a better starting model - use refine2d.py to generate some unbiased class sums, pick a bunch of good classes from the result, and then use startcsym (or is it startAny) to generate a starting model. You should be able to tell if you're getting the off-center problem very early in the refinement - i.e. just do several (or even 1) refinments, and check that the class sums look normal.

-  ⇤ ← Revision 2 as of 2007-11-20 20:24:43 → 
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+   ← Revision 3 as of 2007-11-20 20:29:52 → ⇥
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+'''Answer:''' (Dave, Nov 20th 2007) - This has happened to me before - try generating a better starting model - use refine2d.py to generate some unbiased class sums, pick a bunch of good classes from the result, and then use startcsym (or is it startAny) to generate a starting model. You should be able to tell if you're getting the off-center problem very early in the refinement - i.e. just do several (or even 1) refinments, and check that the class sums look normal.