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@CA,20-30@CA #1: 5-15@CA,20-30@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@CA,20-30@CA #1: 5-15@CA,20-30@CA

then I will get a number

 

If I then run

rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@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@CA,20-30@CA #1: 5-15@CA,20-35@CA

 

This should fail but doesn’t

 

Have I completely misunderstood what Chimera should be doing here?

 

..d