(Bad) Symmetry alignment at the start of jobs (and workaround)

[rbs_sci]

Hi @mmclean,

• Output from VATs:
  

  

• No adjustments to VATs other than specifying octahedral symmetry. The ab initio model had a target res of 6 Å (I find that 6-8 Å gives more reliable initial models for smaller higher symmetry targets).

• Interestingly, 15, 12, and 8 Å starts all align badly and give bad starts (and resulting maps). I tried 15 and 12 Å previously so was expecting that, but wasn’t expecting 8 Å to give a bad start alignment. Also tried 6; same result. But VATs gives a good alignment. Does it search over a larger range of possibilities?

@mmclean

I wonder if some of the discrepancy shown here is due to run-to-run variance (i.e. the volume is aligned in a satisfactory way both times, but due to particle ordering and other random-seed-dependent changes, one job converges and the other doesn’t).

Possibly; maybe related to particle input order? But 99% of the time if I get a good alignment the final model turns out well, even if it takes a while to converge.