VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Apr 03 2014 - 00:40:31 CDT

Hi Charles,

 

please notice that VMD uses STRIDE to determine the secondary structure,
which is using both, hydrogen bonds and torsion angles unlike other tools
that only use the torsions. So if your structure doesn't show the required
hydrogen bonds you may not see any secondary structure or if the angles
aren't exact, a wrong type of helical structure. Also, if you watch per
frame secondary structure of a trajectory you will often see helices
changing from alpha to 3-10 and back temporarily. Please also notice, that
VMD will call STRIDE only once when 1st selected a drawing method like :
Cartoon or Ribbons or if one chooses coloring method: Secondary Structure
and only for the current animation frame. So to get updated SS info for
multiple frames, you might want to have a look at the "sscache" tcl script.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Charles Greenberg
Gesendet: Mittwoch, 2. April 2014 19:40
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: secondary structure inconsistency

 

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:

 

https://www.dropbox.com/s/nwezglwy8kqhs8r/good.pdb

https://www.dropbox.com/s/1f6cx1ij7h4cynn/bad.pdb

 

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

 

Thanks,

Charles 

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