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rcsb / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry
GNU Lesser General Public License v2.1
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CE-Symm uses default max gap size #42

Closed sbliven closed 8 years ago

sbliven commented 9 years ago

CE-CP has always set the max gap size to 0 to allow the large insertions that tend to appear at the CP boundary. However, CE-Symm neglects to make this change, so it uses the default gap size of 30.

sbliven commented 9 years ago

I fixed this in 3800cc04, but it introduced a lot of test changes. There are some minor differences in structures like 1TIM, and some major changes in borderline cases.

Heres some comparisons. The left uses gap=30, and the right gap=0.

1tima gap d1kcwa6_gap d2c35e1_gapchange

lafita commented 9 years ago

Why isn't this change incorporated in the master branch @sbliven?

CESymmParameters continues extending CEParameters instead of CECPParameters. It makes sense to change it, since the algorithm we use is the CECP, and with the refinement I think the results are now more robust to these little differences in the initial alignment.

Should we merge this change?

lafita commented 8 years ago

The CECPParameters gave worst results than the CEParameters, so it was decided to keep them unchanged. Closing this.