[Chimera-users] RMSD Chimera

[Ishita Gupta]

Hi,

I have a few questions in mind regarding rmsd calculation in chimera:

1. Does the matchmaker tool calculate c alpha?
2. Do we consider RMSD of pruned atoms or the total atoms while reporting?
3. If we use structural comparison match align tool then rmsd is based on multiple sequence alignment? And it also gives C alpha?
4. If we calculate rmsd from multi align viewer by clicking on the structure and then match. What these rmsd values denote?

Please elaborate on these points. 

Thanks

Ishita