VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 03 2014 - 11:03:39 CDT

Hi,
  VMD currently calls STRIDE for secondary structure assignment.
The STRIDE algorithm has various floating point thresholds in it, that
can cause an assignment to flip-flop between two outcomes if the input
structure has angles/energies that fall on critical value. Another potential
limitation with STRIDE is that it reads the structure from a PDB-formatted
file, which severely restricts the magnitudes of the atomic coordinates
vs. what might turn up in a simulation trajectory. If your atomic coordinates
are very very far from the origin, the lost precision due to the PDB file
format may impact the quality of the results that STRIDE produces.

We are working on our own replacement for STRIDE that addresses some of
these issues, but it's going to be a few more months before we have something
that's usable yet.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Wed, Apr 02, 2014 at 10:39:33AM -0700, Charles Greenberg wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/