[chimera-dev] Calculating RMSD

[Victor Muñoz]

Hi,

I want to calculate the RMSD between two mol2 structures in place. The two
structures are different forms of the same structure. I haver modified the
mol2 so that the two of them have the same serialNumber in their respective
atoms. The problem is that when I use the command rmsd #model1 #model2, it
return an incorrect value of the rmsd, as the value showed is too high,
about 5, when it should be about 1 (the two structures are very similar). Is
there any way to calculate the RMSD value in place correctly or I am doing
anything wrong?

Thanks for your help.
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