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<p class="MsoNormal">Chimera 1.8 on Windows<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have been trying to align (superimpose) models based on a specific conserved region. Unfortunately Chimera doesn’t seem to do what the documentation claims it does.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I run (example):<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">match #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA <o:p></o:p></p>
<p class="MsoNormal">and get an RMSD calculation (more on this below), but no movement of the model occurs. I specify ‘move true show true’ as options. Still no movement but I have a transformation matrix. Unfortunately this is not in a form that can be understood
by Transform Coordinates.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">How do I persuade my structures to superimpose on the specific atoms?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The RMSD calculation appears to be broken. If I take the command
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA<o:p></o:p></p>
<p class="MsoNormal">then I will get a number<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I then run<o:p></o:p></p>
<p class="MsoNormal">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@CA<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I get exactly the same number. In fact, if I specify atom sets of different sizes (as long as it is not the first block) then I continue to get exactly the same number<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-35@CA<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This should fail but doesn’t<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Have I completely misunderstood what Chimera should be doing here?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">..d<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
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