Houjin How are you determining that the bonds are broken. Can you send me the input and output PDB file along with the version you are using? Nigel On 7/11/2008 4:16 PM, houjin zhang wrote:
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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