Hi, dear folks,

I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation.
I use the following command:

rmsd #0:1.het & ~element.H #1:1.het & ~element.H

But Chimera seems to forget the correct order and give a pairwise alignment not the way I want .
I wonder if there is a way that I can get the correct selection order so as to calculate RMSD.
Best

--
Chao Wu

Currently:
National Institute of Biological Sciences, Beijing
Huang Niu's Lab
http://www.nibs.ac.cn/
Tel: 80726688-8572
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427
Postcode: 102206