[Chimera-users] superimposing two structures based on a specific selection

David Martin d.m.a.martin at dundee.ac.uk
Mon Feb 10 03:08:41 PST 2014

Chimera 1.8 on Windows

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.

I run (example):

match #0:5-15 at CA,20-30 at CA #1: 5-15 at CA,20-30 at CA
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.

How do I persuade my structures to superimpose on the specific atoms?

The RMSD calculation appears to be broken.  If I take the command

rmsd #0:5-15 at CA,20-30 at CA #1: 5-15 at CA,20-30 at CA
then I will get a number

If I then run
rmsd #0:5-15 at CA,20-30 at CA #1: 5-15 at CA,21-31 at CA

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

rmsd #0:5-15 at CA,20-30 at CA #1: 5-15 at CA,20-35 at CA

This should fail but doesn't

Have I completely misunderstood what Chimera should be doing here?


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