Measure Distance
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# This script writes the distance from
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write("%8.3f\n"%dst)
f.close()