Konrad<div><br></div><div>The DCT entry in the phenix copy monomer library is from an earlier version of the monomer library. The newer version of monomer library is likely better but it's not immediately clear that the older version is wrong. Can you send my the .geo file off-list?</div>
<div><br></div><div>Cheers</div><div><br></div><div>Nigel<br><br><div class="gmail_quote">On Tue, Apr 2, 2013 at 9:21 AM, Konrad Bergen <span dir="ltr"><<a href="mailto:Konrad.Bergen@uni-konstanz.de" target="_blank">Konrad.Bergen@uni-konstanz.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello phenixbb,<br>
<br>
i was recently refining a DCT and was a bit puzzled �when i got outliers in torsion angles (readout from the final .geo file). The DCT was built in coot (using the ccp4 monomer library) and seems to fit these restraints. A closer look gave me a discrepancy in the torsion angles between the ccp4 (ver 6.3.0) and the corresponding phenix (dev1325) file<br>
<br>
/usr/local/ccp4-6.3.0/ccp4-6.3.0/lib/data/monomers/d/DCT.cif<br>
<br>
_chem_comp_tor.comp_id<br>
_<a href="http://chem_comp_tor.id" target="_blank">chem_comp_tor.id</a><br>
_chem_comp_tor.atom_id_1<br>
_chem_comp_tor.atom_id_2<br>
_chem_comp_tor.atom_id_3<br>
_chem_comp_tor.atom_id_4<br>
_chem_comp_tor.value_angle<br>
_chem_comp_tor.value_angle_esd<br>
_chem_comp_tor.period<br>
�DCT � � �var_1 � �O3G � �PG � � O3B � �PB � � � -60.011 � 20.000 � 1<br>
�DCT � � �var_2 � �PG � � O3B � �PB � � O3A � � -179.960 � 20.000 � 1<br>
�DCT � � �var_3 � �O3B � �PB � � O3A � �PA � � �-179.992 � 20.000 � 1<br>
�DCT � � �var_4 � �PB � � O3A � �PA � � "O5'" � �179.964 � 20.000 � 1<br>
�DCT � � �var_5 � �O3A � �PA � � "O5'" �"C5'" � �179.986 � 20.000 � 1<br>
�DCT � � �var_6 � �PA � � "O5'" �"C5'" �"C4'" � -179.998 � 20.000 � 1<br>
�DCT � � �var_7 � �"O5'" �"C5'" �"C4'" �"O4'" � � 65.696 � 20.000 � 3<br>
�DCT � � �var_8 � �"C5'" �"C4'" �"C3'" �"C2'" � -150.000 � 20.000 � 3<br>
�DCT � � �var_9 � �"C4'" �"C3'" �"C2'" �"C1'" � � 30.000 � 20.000 � 3<br>
�DCT � � �var_10 � "C5'" �"C4'" �"O4'" �"C1'" � �150.000 � 20.000 � 1<br>
�DCT � � �var_11 � "C4'" �"O4'" �"C1'" �N1 � � �-150.000 � 20.000 � 1<br>
�DCT � � �var_12 � "O4'" �"C1'" �"C2'" �"C3'" � � �0.000 � 20.000 � 3<br>
�DCT � � �var_13 � "O4'" �"C1'" �N1 � � C6 � � �-121.764 � 20.000 � 1<br>
�DCT � � �CONST_1 �"C1'" �N1 � � C2 � � N3 � � � 180.000 � �0.000 � 0<br>
�DCT � � �CONST_2 �"C1'" �N1 � � C6 � � C5 � � � 180.000 � �0.000 � 0<br>
�DCT � � �CONST_3 �N1 � � C6 � � C5 � � C4 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �CONST_4 �C6 � � C5 � � C4 � � N3 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �CONST_5 �C5 � � C4 � � N4 � � HN41 � � 179.773 � �0.000 � 0<br>
�DCT � � �CONST_6 �C5 � � C4 � � N3 � � C2 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �CONST_7 �C4 � � N3 � � C2 � � O2 � � � 180.000 � �0.000 � 0<br>
<br>
<br>
/usr/local/phenix.test/latest/chem_data/mon_lib/d/DCT.cif<br>
<br>
_chem_comp_tor.comp_id<br>
_<a href="http://chem_comp_tor.id" target="_blank">chem_comp_tor.id</a><br>
_chem_comp_tor.atom_id_1<br>
_chem_comp_tor.atom_id_2<br>
_chem_comp_tor.atom_id_3<br>
_chem_comp_tor.atom_id_4<br>
_chem_comp_tor.value_angle<br>
_chem_comp_tor.value_angle_esd<br>
_chem_comp_tor.period<br>
�DCT � � �var_3 � �O1G � �PG � � O3B � �PB � � � � 2.570 � 20.000 � 1<br>
�DCT � � �var_4 � �PG � � O3B � �PB � � O3A � � � 83.412 � 20.000 � 1<br>
�DCT � � �var_6 � �O3B � �PB � � O3A � �PA � � �-132.456 � 20.000 � 1<br>
�DCT � � �var_7 � �PB � � O3A � �PA � � O5* � � �-51.566 � 20.000 � 1<br>
�DCT � � �var_9 � �O3A � �PA � � O5* � �C5* � � -166.199 � 20.000 � 1<br>
�DCT � � �var_10 � PA � � O5* � �C5* � �C4* � � �135.553 � 20.000 � 1<br>
�DCT � � �var_11 � O5* � �C5* � �C4* � �C3* � � � 12.096 � 20.000 � 3<br>
�DCT � � �var_12 � C5* � �C4* � �O4* � �C1* � � �143.686 � 20.000 � 1<br>
�DCT � � �var_13 � C5* � �C4* � �C3* � �C2* � � -117.819 � 20.000 � 3<br>
�DCT � � �var_14 � C4* � �C3* � �C2* � �C1* � � �-21.471 � 20.000 � 3<br>
�DCT � � �var_15 � C3* � �C2* � �C1* � �N1 � � � 150.776 � 20.000 � 3<br>
�DCT � � �var_16 � C3* � �C2* � �C1* � �O4* � � � 32.781 � 20.000 � 3<br>
�DCT � � �var_17 � C2* � �C1* � �N1 � � C2 � � � 121.270 � 20.000 � 1<br>
�DCT � � �var_18 � C2* � �C1* � �N1 � � C6 � � � -65.572 � 20.000 � 1<br>
�DCT � � �CONST_1 �C1* � �N1 � � C2 � � N3 � � � 180.000 � �0.000 � 0<br>
�DCT � � �CONST_2 �N1 � � C2 � � N3 � � C4 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �CONST_3 �C2 � � N3 � � C4 � � C5 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �var_19 � N3 � � C4 � � N4 � � HN41 � � � 0.000 � 20.000 � 1<br>
�DCT � � �CONST_4 �N3 � � C4 � � C5 � � C6 � � � � 0.000 � �0.000 � 0<br>
�DCT � � �CONST_5 �C4 � � C5 � � C6 � � N1 � � � � 0.000 � �0.000 � 0<br>
<br>
I am just wondering which values/library to use or if i got something completely wrong.<br>
Best regards<br>
Konrad<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709� �� Email : NWMoriarty@LBL.gov<br>
Fax�� : 510-486-5909� � �� Web� : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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