<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1415371654838_9789">Hi Team,</div><div id="yui_3_16_0_1_1415371654838_9788" dir="ltr"><br></div><div id="yui_3_16_0_1_1415371654838_9734" dir="ltr">I am trying to align 2 pdb files..</div><div id="yui_3_16_0_1_1415371654838_9747" dir="ltr">When I try to create an object for Bio.PDB.Superimposer(), I get a strange error.</div><div id="yui_3_16_0_1_1415371654838_9805" dir="ltr"><br></div><div id="yui_3_16_0_1_1415371654838_9806" dir="ltr">Langauge specs:<br></div><div id="yui_3_16_0_1_1415371654838_9807" dir="ltr">Python version - 2.7</div><pre id="yui_3_16_0_1_1415371654838_9808" style="" class="">Bio.__version__ - 1.61 ## bio python version</pre><div id="yui_3_16_0_1_1415371654838_9748" dir="ltr">My code looks like:</div><div id="yui_3_16_0_1_1415371654838_9844" dir="ltr"><br></div><div id="yui_3_16_0_1_1415371654838_9809" dir="ltr">from Bio.PDB import * <br></div><div dir="ltr" id="yui_3_16_0_1_1415371654838_9668">def alignPDB_file(refPDB, samplePDB): # function to align pdb file<br style="" class=""> ref_atoms,sample_atoms=[],[]<br style="" class=""><br style="" class=""> ref_model=PDBParser(QUIET=True).get_structure("reference",refPDB)[0] # get the 0th model<br style="" class=""> sam_model=PDBParser(QUIET=True).get_structure("sample",samplePDB)[0] # get the 0th model<br style="" class=""><br style="" class=""> for ref_chain in ref_model:<br style="" class=""> for ref_res in ref_chain:<br style="" class=""> if not "CA" in ref_res:continue<br style="" class=""> else: ref_atoms.append(ref_res['CA']) <br style="" class=""><br style="" class=""> for sam_chain in sam_model:<br style="" class=""> for sam_res in sam_chain:<br style="" class=""> if not "CA" in sam_res: continue<br style="" class=""> else: sample_atoms.append(sam_res['CA'])<br style="" class=""><br style="" class=""> #super_imposer=Bio.PDB.Superimposer()<br style="" class=""> super_imposer = Bio.PDB.Superimposer()<br style="" class=""><br></div><div id="yui_3_16_0_1_1415371654838_9829"><br></div><div id="yui_3_16_0_1_1415371654838_9830" dir="ltr">Error:</div><div id="yui_3_16_0_1_1415371654838_9673" dir="ltr"> super_imposer = Bio.PDB.Superimposer()<br style="" class="">NameError: global name 'Bio' is not defined<br style="" class=""><br></div><div dir="ltr" id="yui_3_16_0_1_1415371654838_9571"><span id="yui_3_16_0_1_1415371654838_9853">Kindly advise.</span></div><br></div></body></html>