[phenixbb] broken bonds in the substrate

[houjin zhang]

Hi:

I am trying to use phenix.elbow to generate restrains for a substrate. I
notice that the PDB file produced by elbow contains  some  broken bonds.  So
I  ran the elbow with the internal strings ATP. The output PDB file also
harbors broken bonds. The --opt did help a little. But some bonds still look
weird. I am wondering if this a bug or I just didn't install phenix right. I
use the latest version of phenix and default setting.

Thank you very much!!

Houjin
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