[Chimera-users] Estimated RMSD after using Modeller feature

[Claudia Fernandes]

I used Modeller function in Chimera to make some comparative models and
then used the estimated RMSD function.

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)?
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.

Any help would be welcome.
Regards,
Cláudia Fernandes
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