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Hi Jack,<br>
<br>
this is a automatic linking bug in 1.11.1_2575 Official Release. I
checked this with the latest code and this does not happen anymore.
<br>
<br>
Anyone else experiencing this problem please update to most recent
nightly build:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/5/17 09:00, Tanner, John J. wrote:<br>
</div>
<blockquote
cite="mid:378C1E79-14A9-43EF-AD27-808B80D3316A@missouri.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear phenix users,�
<div class=""><br class="">
</div>
<div class="">I�m refining a model that has FAD and SO4 ligands.
�Phenix makes a covalent bond between the N3 of the FAD and an O
atom of SO4 during the automatic linking stage, even though the
distance between the atoms is larger than the automatic link
distance. The covalent bond yanks the ligands out of their
density. I suppose I could disable automatic linking, but I�ve
never seen this happen. �I note that we recently upgraded to
phenix-1.11.1-2575, and this may be my first refinement
calculation with the new version. Output is shown below. �
<div class=""><br class="">
</div>
<div class="">I welcome any suggestions. �
<div class=""><br class="">
</div>
<div class="">Thanks,�</div>
<div class=""><br class="">
</div>
<div class="">Jack�</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">-------------------------------------------------------------------------------</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">� PHENIX: Python-based Hierarchical ENvironment
for Integrated Xtallography</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">� Version: 1.11.1</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">� Release tag: 2575</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">� Platform: intel-linux-2.6-x86_64</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">� User: tannerjj</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">-------------------------------------------------------------------------------</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class=""><br class="">
</span></div>
<div class=""><br class="">
</div>
<div class="">---------------------------------------------------------------</div>
<div class="">From the phenix.refine log file:</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">��Automatic linking</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � Parameters for automatic linking</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � Linking & cutoffs</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � � Metal� � � � � � � � : False - 3.50</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � � Amimo acid � � � � � : False - 1.90</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � � Carbohydrate � � � � : True� - 1.99</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � � Ligands� � � � � � � : True� - 1.99</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� � � � Amino acid - RNA/DNA : False</span></div>
<div style="margin: 0px; line-height: normal;
min-height: 13px;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class=""></span><br class="">
</div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Number of custom bonds: simple=2,
symmetry=0</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Number of additional bonds: simple=2,
symmetry=0</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Coordination:</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Other bonds:</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">� �
Simple bond: � pdb=</span><span
style="font-variant-ligatures: no-common-ligatures"
class="">" N3� FAD C 601 "</span><span
style="font-variant-ligatures: no-common-ligatures;
color: #000000" class=""> - pdb=</span><span
style="font-variant-ligatures: no-common-ligatures"
class="">" O2� SO4 F 605 "</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">� �
Simple bond: � pdb=</span><span
style="font-variant-ligatures: no-common-ligatures"
class="">" N3� FAD D 601 "</span><span
style="font-variant-ligatures: no-common-ligatures;
color: #000000" class=""> - pdb=</span><span
style="font-variant-ligatures: no-common-ligatures"
class="">" O4� SO4 F 606 "</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Time building additional restraints: 2.29</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">� Conformation dependent library (CDL)
restraints added in 636.6 milliseconds</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">.</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">.</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">.</span></div>
<div style="margin: 0px; line-height: normal;" class=""><br
class="">
</div>
<div style="margin: 0px; line-height: normal;" class=""><span
style="font-variant-ligatures: no-common-ligatures"
class="">
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">��Bond restraints:
15971</span></div>
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">� Sorted by
residual:</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">�
bond pdb=</span><span
style="font-variant-ligatures:
no-common-ligatures" class="">" N3� FAD D 601 "</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">��
� � pdb=</span><span
style="font-variant-ligatures:
no-common-ligatures" class="">" O4� SO4 F 606 "</span></div>
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">� � ideal� model�
delta� � sigma � weight residual</span></div>
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">� � 1.297� 3.084
-1.787 1.00e-02 1.00e+04 3.19e+04</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">�
bond pdb=</span><span
style="font-variant-ligatures:
no-common-ligatures" class="">" N3� FAD C 601 "</span></div>
<div style="margin: 0px; line-height: normal; color:
rgb(195, 55, 32);" class="">
<span style="font-variant-ligatures:
no-common-ligatures; color: #000000" class="">��
� � pdb=</span><span
style="font-variant-ligatures:
no-common-ligatures" class="">" O2� SO4 F 605 "</span></div>
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">� � ideal� model�
delta� � sigma � weight residual</span></div>
<div style="margin: 0px; line-height: normal;"
class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">� � 1.297� 2.975
-1.678 1.00e-02 1.00e+04 2.81e+04</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class=""><br class="">
</span></div>
<div class="">
<div style="font-family: Helvetica; font-size:
12px;" class="">---------------------------------------------------------------</div>
</div>
<div class=""><br class="">
</div>
<div class="">The output refined PDB file shows the
links were made. The LINK lines were not in the
input PDB file.�</div>
<div class=""><br class="">
</div>
</span></div>
</div>
</div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures; color: #c33720" class="">
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:
no-common-ligatures; background-color: #e6e600"
class="">LINK</span><span
style="font-variant-ligatures: no-common-ligatures"
class=""> � � � � N3� FAD C
</span><span style="font-variant-ligatures:
no-common-ligatures;" class="">601</span><span
style="font-variant-ligatures: no-common-ligatures"
class=""> � � � � � � � � O2� SO4 F
</span><span style="font-variant-ligatures:
no-common-ligatures;" class="">605</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:
no-common-ligatures; background-color: #e6e600"
class="">LINK</span><span
style="font-variant-ligatures: no-common-ligatures"
class=""> � � � � N3� FAD D
</span><span style="font-variant-ligatures:
no-common-ligatures;" class="">601</span><span
style="font-variant-ligatures: no-common-ligatures"
class=""> � � � � � � � � O4� SO4 F
</span><span style="font-variant-ligatures:
no-common-ligatures;" class="">606</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<br class="">
</div>
<div style="color: rgb(0, 0, 0); font-family: Menlo;
font-size: 11px;" class="">
<div style="font-family: Helvetica; font-size: 12px;"
class="">---------------------------------------------------------------</div>
</div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:
no-common-ligatures;" class=""><br class="">
</span></div>
<div style="margin: 0px; font-size: 11px; line-height:
normal; font-family: Menlo;" class="">
<br class="">
</div>
</span></div>
<div class="">
<div class="">
<div style="orphans: 2; widows: 2;" class="">John J.
Tanner, PhD<br class="">
Professor of�Biochemistry�and�Chemistry</div>
<div style="orphans: 2; widows: 2;" class="">Director,
Biochemistry Graduate Admissions Committee</div>
<div style="orphans: 2; widows: 2;" class="">Department
of Biochemistry</div>
<div style="orphans: 2; widows: 2;" class="">University
of Missouri-Columbia<br class="">
117 Schweitzer Hall<br class="">
503 S. College Avenue<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280<br class="">
Fax: 573-882-2754<br class="">
Email:�<a moz-do-not-send="true"
href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br
class="">
<a moz-do-not-send="true"
href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
</div>
<div class=""><br class="">
</div>
<br class="Apple-interchange-newline">
</div>
<br class="">
</div>
</div>
</div>
<br>
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