Hi..<br>
<br>
I am doing advance modelling with multiple template . I have to add ATP
ang Mg in my structure . I am trying to add @ , $ for the purpose ,ATP
hetero atom is present in the template even though its giving error .<br>
<br>
Can I add ATP in 1 of the template only .<br>
<br>
<span style="color: rgb(255, 0, 0);">The error is -&nbsp; </span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">File &quot;model_mult.py&quot;, line 9, in ?</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp;&nbsp;&nbsp; a.make()</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp; File &quot;/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py&quot;, line 108, in make</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp;&nbsp;&nbsp; self.homcsr(exit_stage)</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp; File &quot;/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py&quot;, line 416, in homcsr</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp;&nbsp;&nbsp; aln.check()</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp; File &quot;/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/alignment.py&quot;, line 154, in check</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">&nbsp;&nbsp;&nbsp; libs=self.env.libs.modpt)</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">_modeller.error: rdabrk__337E&gt; Structure not read in...<br>
<br>
The log file is - <br>
<br>
runcmd______&gt; alignment.append(align_codes=[&#39;2FFAA&#39;, &#39;1XEFA&#39;,
&#39;2FFBA&#39;, &#39;CaNBD&#39;], atom_files=[], file=&#39;CaNBD-mult.ali&#39;,
(def)remove_gaps=True, (def)alignment_format=&#39;PIR&#39;,
(def)rewind_file=False, (def)close_file=True)<br>
read_te_290E&gt; Number of residues in the alignment and&nbsp; pdb
files are different:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
242&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 241<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
For alignment entry:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;
1XEFA<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x&nbsp; (mismatch at alignment position&nbsp;&nbsp;&nbsp; 242)<br>
&nbsp;Alignment&nbsp;&nbsp;
KELLSEPESLYSYLYQLQSD@&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PDB&nbsp;&nbsp;
KELLSEPESLYSYLYQLQSD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<br>
&nbsp;&nbsp;&nbsp;&nbsp; Match&nbsp;&nbsp; ********************<br>
<br>
&nbsp; Please check your alignment file header to be sure you correctly specified<br>
&nbsp; the starting and ending residue numbers and chains. The alignment sequence<br>
&nbsp; must match that from the atom file exactly.<br>
<br>
&nbsp; Another possibility is that some residues in the atom file are missing,<br>
&nbsp; perhaps because they could not be resolved experimentally. (Note that Modeller<br>
&nbsp; reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)<br>
&nbsp; In this case, simply replace the section of your alignment corresponding<br>
&nbsp; to these missing residues with gaps.<br>
read_te_288W&gt; Protein not accepted:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp; 1XEFA<br>
rdabrk__337E&gt; Structure not read in (please consult the log file<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; for more details):<br style="color: rgb(255, 0, 0);">
</span><br>
<br>
<br>
Please help.<br clear="all"><br>Thanks and Regards<br>
<br>
Ajeeta kaushiki<br>
JNU<br>