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channotation / chap

CHAP is a tool for the functional annotation of ion channel structures:
http://www.channotation.org
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how to set pf-init-probe-pos? #43

Closed ncoudray closed 2 years ago

ncoudray commented 2 years ago

Hi,

I can't figure out how to set the "-pf-init-probe-pos". I tried to get the coordinates from chimera, but I keep getting either:

Reading frames from pdb fileWARNING: all CONECT records are ignored
Reading frame       0 time   -1.000   Segmentation fault

or

Pore radius at initial probe position is infinite. Consider increasing the
maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for
neighbourhood searches explicitly with -pf-cutoff.

Maybe I get the coordinate position system wrong? Can you please let me know how to figure out what values put here?

Thanks, Best, Nicolas

ncoudray commented 2 years ago

Nevermind, I found coordinates should be in nm, not Angs