<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1431012741521_2484">Hi!</div><div id="yui_3_16_0_1_1431012741521_2484"><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr">I am new to Chimera and I am trying to modify the PDB file of a peptide by acylation. I have also a PDB file for the fatty acid which I got by removing the bound protein. I used the join models to form a peptide bond but prompted with this error:</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr"><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr"><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr"> The following problems occurred while reading PDB file for anomt1.pdb</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Start residue of secondary structure not found: HELIX 1 1 LEU 2 LEU 10 1 8</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Model 1 (anomt1.pdb) appears to be a protein without secondary structure assignments.</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Automatically computing assignments using 'ksdssp' and parameter values:</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> energy cutoff -0.5</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> minimum helix length 3</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> minimum strand length 3</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Use command 'help ksdssp' for more information.</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">TypeError Exception in Tk callback</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> Function: <bound method BuildStructureDialog._addParamBond of <BuildStructure.gui.BuildStructureDialog object at 0x04F9FBF0>> (type: <type 'instancemethod'>)</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> Args: ()</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Traceback (innermost last):</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> return apply(self.func, args)</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\gui.py", line 313, in _addParamBond</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> self._appbDihedral.get(), phi=self._appbPhi.get())</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\__init__.py", line 869, in cnPeptideBond</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> cn[1].residue.phi = phi</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 91, in setPhi</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> _setAngle(bond, phi, getPhi(res), "phi")</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> br.angle = (newAngle - curAngle, br.biggerSide())</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""><br class="" style=""></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""><br class="" style=""></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""> br.angle = (newAngle - curAngle, br.biggerSide())</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">My first question is how to solve this error. Second, how can I optimize the generated PDB file using Chimera? I want also to convert this optimize PDB file to PQR.</div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style=""><br></div><div id="yui_3_16_0_1_1431012741521_2484" dir="ltr" class="" style="">Any advice is greatly appreciated.</div></div></body></html>