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== v2.5 flag ignore updates == I've updated the CLI examples so that they should behave consistently since the v2.5 update to the treatment of flag ignore. Basically, flag ignore does what it should, but the previously magically ignored solvent molecules are now no longer magically ignored so need to be specifically excluded. I haven't fixed the script example yet for per-residue SASA, but I suspect that it also needs a "flag ignore, solvent" adding.
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