Hi again

Oh, you don't need to change all your model files.
The setting may go in your page, there are several ways to do it

I've looked at you demo page and file
Yes, it seems you are in the limit!

distance        1.86    0.186 nm        C8/1 #8         P4/1 #4    // bonded
distance        1.92    0.192 nm        C10/1 #10       P4/1 #4    // not bonded
distance        1.92    0.192 nm        C9/1 #9         P4/1 #4    // not bonded

You can do this:

jmolApplet(600, "set bondTolerance 0.6; load tBuPCPIr.log.gz; cpk 25%");


default seems to be bondTolerance = 0.45



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