VMD-L Mailing List

From: Charles Greenberg (greenberg.charles.h_at_gmail.com)
Date: Thu Apr 03 2014 - 12:48:16 CDT

OK that answer makes a lot of sense, thank you John. I've had more
consistency viewing the structure in Chimera, which uses DSSP, if that's
any help.

On Thu, Apr 3, 2014 at 9:03 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>