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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thankyou - it was my misreading of the atom specification pages that has lead to this issue.
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks for your help.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..d<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Tom Goddard [mailto:goddard@sonic.net]
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<b>Sent:</b> 10 February 2014 18:29<br>
<b>To:</b> David Martin<br>
<b>Cc:</b> 'chimera-users@cgl.ucsf.edu'<br>
<b>Subject:</b> Re: [Chimera-users] superimposing two structures based on a specific selection<o:p></o:p></span></p>
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<p class="MsoNormal">Hi David,<o:p></o:p></p>
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<p class="MsoNormal"> I tried exactly your command in Chimera 1.8 with two randomly chosen model (3pfj, 2gbp) and match worked as expected (after removing the space after "#1:" which gives an error). So to know why your case does not work we'd need the actual
PDB models you are using. But without those here is my suspicion. The match doesn't move the first model because it is already aligned. You could test this by moving one model relative to the other, then try the command again (use the Active buttons in
Model Panel to freeze one model, then move the other with the mouse).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Also the specifier "#0:5-15@CA,20-30@CA" has the wrong syntax. It should be #0:5-15@CA:20-30@CA" (with the comma replaced by a colon). The first specifier will only select the 11 CA atoms 5-15 because with the comma it says take atoms
named CA and atoms named "20-30" and atoms named CA. There are no atoms named "20-30". This explains why your rmsd values don't depend on the 20-30 or 21-31 or 20-35.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Here is some documentation on atom specifiers<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Note that the 7th example is the same kind of specifier you were attempt with two residue ranges.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Feb 10, 2014, at 3:08 AM, David Martin <<a href="mailto:d.m.a.martin@dundee.ac.uk">d.m.a.martin@dundee.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Chimera 1.8 on Windows<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I run (example):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">match #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">How do I persuade my structures to superimpose on the specific atoms?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">The RMSD calculation appears to be broken. If I take the command<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">then I will get a number<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">If I then run<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@CA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-35@CA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">This should fail but doesn’t<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Have I completely misunderstood what Chimera should be doing here?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">..d<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><br>
</span><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span class="apple-converted-space"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""> </span></span><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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