VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 16 2017 - 14:46:55 CDT

Hi,
  Several things can cause STRIDE not to assign a secondary structure:
- non-writable /tmp or /usr/tmp (what is your $TMPDIR set to?)
- atom names that are not recognized by STRIDE. STRIDE assumes PDB-derived
  atom names are used, and it will often fail if some atoms are unrecognized.
- coordinates are shifted very far away from the origin (thus exceeding the
  PDB file format coordinate field widths, since the PDB format is
  used to communicate with STRIDE).
- STRIDE really only understands proteins, and it may get upset about
  some unusual structures where proteins are bonded to small pieces of
  nucleic acid, or the like.
- I'm sure I've forgotten some other issues/situations that can
  upset STRIDE, these are meant to be exemplary...

You can eliminate most of the oddball issues by checking against a
structure that is known to work fine with STRIDE under normal circumstances,
and if that doesn't work, then you should see if there is an issue with
directory writability or other system-level issues that are not related
to the particular molecular system you are studying.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 16, 2017 at 06:11:38PM +0000, Vermaas, Joshua wrote:
> Hi Steve,
>
> If you just get a stringy mess, it means that STRIDE failed. STRIDE is the program VMD uses for secondary structure assignment, and if it fails, VMD assumes everything is unstructured. Usually I can get it to work if I feed in correct bond information into VMD by loading a psf in addition to a pdb, but that really depends on the structure.
>
> -Josh
>
> On 06/16/2017 10:51 AM, Seibold, Steve Allan wrote:
>
> HI vmd users...
>
> I notice some people have reported similar problems as list below. However, I have just started having this problem without reinstalling anything. Vmd WAS running just fine and then suddenly I stopped getting secondary structures with "NewCartoon". I just get strings....
>
>
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
>
>
> My Xversion is:
>
> version number 11.0
>
> X.Org version 1.18.4
>
>
> My OS is Ubuntu 16.04
>
>
> Does anyone have any information about this problem???
>
>
> Thanks Steve
>
> 

-- 
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/