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</o:shapelayout></xml><![endif]--></head><body lang=ZH-TW link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Dear all,<o:p></o:p></span></p><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3 at C2’. <o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>I gave the se labeled pdb structure to the Elbow or ReadySet, the program gave me the cif as shown below. <o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>When I tried to refine the structure, phenix.refine ends with a Error message:<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Chain: "A"<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Number of atoms: 23<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Number of conformers: 1<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Conformer: ""<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Number of residues, atoms: 1, 23<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Unexpected atoms: {'AMS,OP1': 1, 'AMS,OP2': 1}<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Classifications: {'DNA': 1}<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Unresolved non-hydrogen bonds: 2<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Unresolved non-hydrogen angles: 3<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Unresolved non-hydrogen chiralities: 1<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> Number of atoms with unknown nonbonded energy type symbols: 2<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> "HETATM 2 OP1 AMS A 1 .*.A O "<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'> "HETATM 3 OP2 AMS A 1 .*.A O "<o:p></o:p></span></pre><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>Any advice on how to modified the cif or pdb files?<o:p></o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>Thanks so much in advance.</span><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p></o:p></span></pre><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>CIF files: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS P P P . 10.3639 38.8090 53.6083<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS OP1 O OH1 . 9.8621 39.4308 52.7650<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS OP2 O O . 9.6270 38.9790 55.3430<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS O5' O O2 . 11.5188 37.6926 53.7178<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C5' C CH2 . 12.2621 37.6244 54.8065<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C4' C CR15 . 13.5128 36.9044 54.7141<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS O4' O O . 14.2653 37.1385 55.8584<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C3' C CR15 . 13.2442 35.4155 54.6698<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS O3' O OH1 . 14.1003 34.8289 53.7923<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C2' C CR15 . 13.5010 34.9324 55.9516<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS SE2' SE SE . 11.8697 34.2402 56.7089<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C1' C CR15 . 13.9654 36.1199 56.7679<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS CA' C CH3 . 11.5566 32.3937 56.0481<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N9 N NR5 . 15.1526 35.8937 57.6065<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C8 C CR15 . 16.4077 35.6661 57.1789<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N7 N N . 17.1943 35.5119 58.2703<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C5 C CR56 . 16.4320 35.6429 59.3887<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C4 C CR56 . 15.1196 35.8884 58.9705<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N1 N N . 15.6651 35.7647 61.7193<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C2 C CR16 . 14.4119 35.9994 61.2874<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N3 N N . 14.1134 36.0657 59.9478<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C6 C CR6 . 16.7122 35.5796 60.8007<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N6 N NH2 . 18.1110 35.3174 61.2840<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>#<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>loop_<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.comp_id<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.atom_id_1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.atom_id_2<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.type<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.value_dist<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>_chem_comp_bond.value_dist_esd<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS P OP1 single 1.162 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS P OP2 double 1.892 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS P O5' single 1.610 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS O5' C5' single 1.320 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C5' C4' single 1.446 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C4' O4' single 1.389 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C4' C3' single 1.514 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS O4' C1' single 1.398 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C3' O3' single 1.359 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C3' C2' single 1.394 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C2' SE2' single 1.927 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C2' C1' single 1.514 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS SE2' CA' single 1.986 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C1' N9 single 1.471 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N9 C8 aromatic 1.345 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N9 C4 aromatic 1.364 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C8 N7 aromatic 1.354 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N7 C5 aromatic 1.360 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C5 C4 aromatic 1.399 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C5 C6 aromatic 1.441 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C4 N3 aromatic 1.414 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N1 C2 aromatic 1.346 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS N1 C6 aromatic 1.405 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C2 N3 aromatic 1.374 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>AMS C6 N6 single 1.503 0.02<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'>Best Regards</span><span lang=EN-US style='font-family:"Times New Roman","serif";color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Lauren <o:p></o:p></span></p></div></body></html>