<div dir="ltr"><div class="gmail_extra">Juanxun</div><div class="gmail_extra"><br></div><div class="gmail_extra">Sorry for the slow response but you don't need to use the apply_cif_link because the links are automatically applied in phenix.refine.</div>
<div class="gmail_extra"><br></div><div class="gmail_extra" style>You can check this using the .geo file thus</div><div class="gmail_extra" style><br></div><div class="gmail_extra" style><div class="gmail_extra">elbow.refine_geo_display PHE-SEP-ARG_minimized.geo SEP !</div>
<div class="gmail_extra"><br></div><div class="gmail_extra" style>The output (see below) shows the restraints between SEP and anything else. The first RMS section is the entire model, the second is for the selection.</div>
<div class="gmail_extra" style><br></div><div class="gmail_extra" style>In the latest�nightly�builds, there is also a graphical representation available via REEL.</div><div class="gmail_extra" style><br></div><div class="gmail_extra" style>
phenix.reel PHE-SEP-ARG_minimized.pdb PHE-SEP-ARG_minimized.geo</div><div class="gmail_extra" style><br></div><div class="gmail_extra" style>Cheers</div><div class="gmail_extra" style><br></div><div class="gmail_extra" style>
Nigel</div><div class="gmail_extra"><br></div><div class="gmail_extra">RMS results for model</div><div class="gmail_extra"><br></div><div class="gmail_extra">RMS(D/Z)</div><div class="gmail_extra">� � � � � � �d-all � � � � �d-none � � � � d-alt � � � � �z-all � � � � �z-none � � � � z-alt � � � � �</div>
<div class="gmail_extra">� bond � � � 0.001( � 32) � 0.001( � 32) � 0.000( � �0) � 0.024( � 32) � 0.024( � 32) � 0.000( � �0)</div><div class="gmail_extra">� angle � � �0.216( � 42) � 0.216( � 42) � 0.000( � �0) � 0.080( � 42) � 0.080( � 42) � 0.000( � �0)</div>
<div class="gmail_extra">----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds�</div><div class="gmail_extra">� �1 " C � PHE C � 3 " - " N � SEP C � 4 " ['1.329', '1.329', '-0.000', '1.40e-02', '5.10e+03', '3.76e-04']</div>
<div class="gmail_extra">� �2 " C � SEP C � 4 " - " N � ARG C � 5 " ['1.329', '1.329', '-0.000', '1.40e-02', '5.10e+03', '5.93e-05']</div><div class="gmail_extra">
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles�</div><div class="gmail_extra">� �1 " C � PHE C � 3 " - " N � SEP C � 4 " - " CA �SEP C � 4 " ['121.70', '121.80', '-0.10', '1.80e+00', '3.09e-01', '3.34e-03']</div>
<div class="gmail_extra">� �2 " CA �PHE C � 3 " - " C � PHE C � 3 " - " N � SEP C � 4 " ['116.20', '116.25', '-0.05', '2.00e+00', '2.50e-01', '6.82e-04']</div>
<div class="gmail_extra">� �3 " C � SEP C � 4 " - " N � ARG C � 5 " - " CA �ARG C � 5 " ['121.70', '121.73', '-0.03', '1.80e+00', '3.09e-01', '2.87e-04']</div>
<div class="gmail_extra">� �4 " CA �SEP C � 4 " - " C � SEP C � 4 " - " N � ARG C � 5 " ['116.20', '116.23', '-0.03', '2.00e+00', '2.50e-01', '2.85e-04']</div>
<div class="gmail_extra">� �5 " O � PHE C � 3 " - " C � PHE C � 3 " - " N � SEP C � 4 " ['123.00', '123.01', '-0.01', '1.60e+00', '3.91e-01', '1.81e-05']</div>
<div class="gmail_extra">� �6 " O � SEP C � 4 " - " C � SEP C � 4 " - " N � ARG C � 5 " ['123.00', '123.00', '0.00', '1.60e+00', '3.91e-01', '5.79e-07']</div>
<div class="gmail_extra">---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals�</div><div class="gmail_extra">� �1 " CA �PHE C � 3 " - " C � PHE C � 3 " - " N � SEP C � 4 " - " CA �SEP C � 4 " ['180.00', '-179.13', '-0.87', '0', '5.00e+00', '4.00e-02', '3.05e-02']</div>
<div class="gmail_extra">� �2 " CA �SEP C � 4 " - " C � SEP C � 4 " - " N � ARG C � 5 " - " CA �ARG C � 5 " ['180.00', '-179.41', '-0.59', '0', '5.00e+00', '4.00e-02', '1.38e-02']</div>
<div class="gmail_extra">---- chirals ---- chirals ---- chirals ---- chirals ---- chirals ---- chirals�</div><div class="gmail_extra"><br></div><div class="gmail_extra">RMS results for selection</div><div class="gmail_extra">
<br></div><div class="gmail_extra">RMS(D/Z)</div><div class="gmail_extra">� � � � � � �d-all � � � � �d-none � � � � d-alt � � � � �z-all � � � � �z-none � � � � z-alt � � � � �</div><div class="gmail_extra">� bond � � � 0.000( � �2) � 0.000( � �2) � 0.000( � �0) � 0.000( � �2) � 0.000( � �2) � 0.000( � �0)</div>
<div class="gmail_extra">� angle � � �0.054( � �6) � 0.054( � �6) � 0.000( � �0) � 0.029( � �6) � 0.029( � �6) � 0.000( � �0)</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br></div></div><div class="gmail_extra">
<br></div><div class="gmail_extra">Nigel</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 21, 2013 at 10:51 PM, Jianxun Qi <span dir="ltr"><<a href="mailto:jxqi@im.ac.cn" target="_blank">jxqi@im.ac.cn</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div>refinement.pdb_interpretation {<br>� apply_cif_link
{<br>��� data_link = "SEPC-N"<br>���
residue_selection_1 = "chain C and resname PHE and resid
3"<br>��� residue_selection_2 = "chain C and resname SEP and
resid 4"<br>� }<br>� apply_cif_link {<br>��� data_link
= "SEPC-N"<br>��� residue_selection_1 = "chain C and resname SEP
and resid 4"<br>��� residue_selection_2 = "chain C and resname
ARG and resid 5"<br>� }<br>}</div></blockquote></div><br><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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