[phenixbb] broken bonds in the substrate

[Nigel W. Moriarty]

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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>
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-- 
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 : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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