<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>[chimera-dev] Calculating RMSD</div><div><br></div><div>Hi,<br><br>I want to calculate the RMSD between two mol2 structures in place. The two<br>structures are different forms of the same structure. I haver modified the<br>mol2 so that the two of them have the same serialNumber in their respective<br>atoms. The problem is that when I use the command rmsd #model1 #model2, it<br>return an incorrect value of the rmsd, as the value showed is too high,<br>about 5, when it should be about 1 (the two structures are very similar). Is<br>there any way to calculate the RMSD value in place correctly or I am doing<br>anything wrong?<br><br>Thanks for your help.</div><div><br></div><div>
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