Hi,<div><br></div><div>I am working on the 1qg8 example given at <a href="http://salilab.org/modeller/wiki/Missing%20residues">http://salilab.org/modeller/wiki/Missing%20residues</a>. I am trying to read the HETATM records and the waters.</div>
<div><br></div><div>Here is my alignment file.</div><div><br></div><div><div><font color="#000099">&gt;P1;1qg8</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">structureX:1qg8:   2 :A:+661 :A:MOL_ID  1; MOLECULE  SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN  A; ENGINEERED  YES; OTHER_DETAILS  GLYCEROL MAGNESIUM:MOL_ID  1; ORGANISM_SCIENTIFIC  BACILLUS SUBTILIS; GENE  SPSA; EXPRESSION_SYSTEM  ESCHERICHIA COLI; EXPRESSION_SYSTEM_STRAIN  BL 21: 1.50: 0.16</font></div>
<div><font color="#000099"><br></font></div><div><font color="#000099">PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW</font></div>
<div><font color="#000099"><br></font></div><div><font color="#000099">NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT---------</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">-----EFVRNLPPQRNCRELRESLKKLGMG...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww</font></div>
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<div><font color="#000099"><br></font></div><div><font color="#000099">&gt;P1;1qg8_fill</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">sequence:::::::::</font></div><div><font color="#000099"><br>
</font></div><div><font color="#000099">PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW</font></div>
<div><font color="#000099"><br></font></div><div><font color="#000099">NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF</font></div><div><font color="#000099"><br></font></div><div><font color="#000099">ELEKNEFVRNLPPQRNCRELRESLKKLGMG...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww</font></div>
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</div><div><font color="#000099"><br></font></div><div>I have run the python script and get an error like this.</div><div><font color="#000099"><br></font></div><div><div style="color:rgb(0,0,153)">Read the alignment from file       : 1qg8.ali</div>
<div style="color:rgb(0,0,153)">Total number of alignment positions:   678</div><div style="color:rgb(0,0,153)"><br></div><div style="color:rgb(0,0,153)">  #  Code        #_Res #_Segm PDB_code    Name</div><div style="color:rgb(0,0,153)">
-------------------------------------------------------------------------------</div><div style="color:rgb(0,0,153)">  1       1qg8     661      1        1qg8 MOL_ID  1; MOLECULE  SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN</div>
<div style="color:rgb(0,0,153)">  2  1qg8_fill     678      1</div><div style="color:rgb(0,0,153)">check_a_343_&gt; &gt;&gt; BEGINNING OF COMMAND</div><div style="color:rgb(0,0,153)">openf___224_&gt; Open           .\1qg8.pdb</div>
<div style="color:rgb(0,0,153)"><br></div><div style="color:rgb(0,0,153)">Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:       805668     786.785     0.768</div><div style="color:rgb(0,0,153)">read_pd_459W&gt; Residue type  GOL not recognized. &#39;automodel&#39; model building</div>
<div style="color:rgb(0,0,153)">              will treat this residue as a rigid body.</div><div style="color:rgb(0,0,153)">              To use real parameters, add the residue type to ${LIB}/restyp.lib,</div><div style="color:rgb(0,0,153)">
              its topology to ${LIB}/top_*.lib, and suitable forcefield</div><div style="color:rgb(0,0,153)">              parameters to ${LIB}/par.lib.</div><div style="color:rgb(0,0,153)">read_te_290E&gt; Number of residues in the alignment and  pdb files are different:      661      637</div>
<div style="color:rgb(0,0,153)">              For alignment entry:        1  1qg8</div><div style="color:rgb(0,0,153)">                                 x  (mismatch at alignment position    638)</div><div style="color:rgb(0,0,153)">
 Alignment   wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww                 </div><div style="color:rgb(0,0,153)">       PDB   wwwwwwwwwwwwwwwwwwww                                         </div><div style="color:rgb(0,0,153)">
     Match   ********************</div><div style="color:rgb(0,0,153)"><br></div><div style="color:rgb(0,0,153)">  Please check your alignment file header to be sure you correctly specified</div><div style="color:rgb(0,0,153)">
  the starting and ending residue numbers and chains. The alignment sequence</div><div style="color:rgb(0,0,153)">  must match that from the atom file exactly.</div><div style="color:rgb(0,0,153)"><br></div><div style="color:rgb(0,0,153)">
  Another possibility is that some residues in the atom file are missing,</div><div style="color:rgb(0,0,153)">  perhaps because they could not be resolved experimentally. (Note that Modeller</div><div style="color:rgb(0,0,153)">
  reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)</div><div style="color:rgb(0,0,153)">  In this case, simply replace the section of your alignment corresponding</div><div style="color:rgb(0,0,153)">
  to these missing residues with gaps.</div><div style="color:rgb(0,0,153)">read_te_288W&gt; Protein not accepted:        1  1qg8</div><div style="color:rgb(0,0,153)"><br></div><div>The pdb file has 661 residues and 17 are missing. To read the hetatm records I have used &#39;.&#39; and for the waters I have used &#39;w&#39;. Could you please tell me where I have gone wrong?</div>
<div><br></div><div>Thank you very much</div><div><br></div><div>Sajeewa Dewage</div><div style="color:rgb(0,0,153)"><br></div></div>