[Chimera-users] Calculating RMSD for ligand

吴超 lynnwuchao at gmail.com
Sat Sep 27 07:04:56 PDT 2008

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.

Chao Wu

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