I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function.<div><br></div><div>I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)?</div>
<div>As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it.</div><div><br></div><div>Any help would be welcome.</div><div>
Regards,</div><div>Cláudia Fernandes</div>