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Houjin<br>
<br>
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?<br>
<br>
Nigel<br>
<br>
On 7/11/2008 4:16 PM, houjin zhang wrote:
<blockquote
cite="mid:6495f89e0807111616x6b56f2a6s852aa82a22b36a12@mail.gmail.com"
type="cite">Hi:<br>
<br>
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.<br>
<br>
Thank you very much!!<br>
<br>
Houjin<br>
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<pre class="moz-signature" cols="72">--
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 : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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