Dear Modellers,<br><br>I&#39;m building a heterodimer with a homodimer template. I have the template pdb file (dimer.pdb) and the sequence file of the heterodimer (hetero.ali).<br><br>Here is the hetero.ali file:<br><br>&gt;P1;hetero<br>
sequence:to_model:1:A:859:B:853::: <br>AAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBB<br><br><br>There are 859 a.a. in one chain and 853 a.a. in the other chain. I didn&#39;t type the exact number of a.a. here.<br><br>The following is the script I used for alignment:<br>
<br>from modeller import *<br><br>env = environ()<br>aln = alignment(env)<br>mdl = model(env, file=&#39;dimer&#39;, model_segment=(&#39;FIRST:A&#39;,&#39;LAST:A&#39;))<br>aln.append_model(mdl, align_codes=&#39;dimerAB&#39;, atom_files=&#39;dimer.pdb&#39;)   # I used &quot;dimerAB&quot; to point out both chain A and chain B for alignment. I don&#39;t know whether it is correct.<br>
aln.append(file=&#39;hetero.ali&#39;, align_codes=&#39;hetero&#39;)<br>aln.align2d()<br>aln.write(file=&#39;hetero-dimerAB.ali&#39;, alignment_format=&#39;PIR&#39;)<br>aln.write(file=&#39;hetero-dimerAB.pap&#39;, alignment_format=&#39;PAP&#39;)<br>
<br><br>The script running result showed the two chain of the heterodimer aligned to one chain of the template. Would you kindly tell me how I can get the correct alignment? Thank you.<br><br><br>Xiongzhuo Gao<br><br>BMCB Department<br>
University of New Hampshier<br>Durham, New Hampshire 03824<br><br><br><br>