Hi,<br><br>Now the scripts are working. Log files are being generated successfully.<br><br>I am trying to use complete_pdb.py to add missing atoms to my pdbfile.<br><br>Here is the command i am using<br><br>mod9v5 complete_pdb.py (ChainA.pdb)<br>
<br>The following log file is being generated<br><br><font size="1">MODELLER 9v5, 2008/10/07, r6498<br><br>&nbsp;&nbsp;&nbsp;&nbsp; PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS<br><br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Copyright(c) 1989-2008 Andrej Sali<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; All Rights Reserved<br><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; Written by A. Sali<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; with help from<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sanchez, B. Yerkovich, A. Badretdinov,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F. Melo, J.P. Overington, E. Feyfant<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; University of California, San Francisco, USA<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Rockefeller University, New York, USA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Harvard University, Cambridge, USA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imperial Cancer Research Fund, London, UK<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Birkbeck College, University of London, London, UK<br>
<br><br>Kind, OS, HostName, Kernel, Processor: 4, Windows Vista build 6001 Service Pack 1, EINSTEIN, SMP, x86 Family 6 Model 14 Stepping 12<br><br>Date and time of compilation&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2008/10/07 16:19:49<br>MODELLER executable type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : i386-w32<br>
Job starting time (YY/MM/DD HH:MM:SS): 2009/01/08 00:07:19<br><br>Total CPU time [seconds]&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; 0.22<br><br></font><br>I have been using the following link <a href="http://salilab.org/modeller/manual/node403.html">http://salilab.org/modeller/manual/node403.html</a><br>
<br>Am i missing something.<br><br>Please help me how to use it.<br><br>Regards,<br><br>Sarath<br><div class="gmail_quote">On Wed, Jan 7, 2009 at 4:28 PM, Modeller Caretaker <span dir="ltr">&lt;<a href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">Sarath Chandra wrote:<br>
&gt; I am Sarath and i am an intern in Max Planck Institute of Biophysical<br>
&gt; Chemistry Gottingen. I am working on Molecular Dynamic simulations of<br>
&gt; Photosystem II a membrane protein which has 17 subunits and all of these<br>
&gt; subunits has all together 200 atoms missing.<br>
&gt;<br>
&gt; I am trying to use complete_pdb.py &nbsp;and i am facing an error &quot;import<br>
&gt; site failed;&quot;<br>
&gt;<br>
&gt; Any suggestions on a the problem and how to use the script<br>
<br>
</div>See #2 at <a href="http://salilab.org/modeller/release.html#issues" target="_blank">http://salilab.org/modeller/release.html#issues</a><br>
<br>
The script should still run fine, despite that warning.<br>
<br>
 &nbsp; &nbsp; &nbsp; &nbsp;Ben Webb, Modeller Caretaker<br>
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