[phenixbb] broken bonds in the substrate
zhanghoujin at gmail.com
Fri Jul 11 16:16:25 PDT 2008
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!!
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