VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jun 16 2017 - 13:11:38 CDT

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