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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I have about 150 peptide structures in PDB format. I would
like to compare each of them with a Template Structure (also in PDB format) and
obtain an RMSD measurement for each comparison. </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>These peptides are similar in structures to the template but
may have very low sequence similarity/conservation.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>So my question is:</span></font></p>
<ol start=1 type=1>
<li class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>what is the command I should use given this scenario..?
I was quite confused with the many different commands such as: <i><span
style='font-style:italic'>rmsd, match, ensemblematch, matchmaker,…</span></i>
can anyone enlighten me on the differences among them. I would like to
find one which can align/superimpose 2 peptides and calculate RMSD (Ca or
backbone)</span></font></li>
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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<ol start=2 type=1>
<li class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Is there a way to automate the process through
scripting..?</span></font></li>
</ol>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I’m still young with CHIMERA so please pardon my
ignorance. =]</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Cheers,</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sum</span></font></p>
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