From: Charles Greenberg (
Date: Wed Apr 02 2014 - 12:39:33 CDT

VMD is giving me inconsistent calculations of secondary structure. For my
protein, some alpha_helix regions are being rendered as helix_3_10 or just
unstructured. What makes this really strange is that if I do a rigid body
rotation of this protein (in another program), the transformed pdb has
correct secondary structure! These pdb files are identical except for that
rigid body transform. Am I doing something wrong?

The two PDB files are available here:

I find this problem in VMD 1.9.1 both on Linux and Mac.