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 ------------------------------------------------------------------------

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov