From: David Carrasco de Busturia (
Date: Sat Nov 19 2022 - 05:48:51 CST

Methods `Coloring Method=Secondary Structure`
`Drawing Method=NewCartoon` or `NewRibbons`
fail with the latest version of Mesa, that being 22.2.3 (dated 2022-11-07)
on vmd 1.9.4a57.

I'm running Linux.

*Minimal Working Example:*

Download pdb from here:;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkAzTKxRX$

Otherwise, you can also find it here:;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkMEmpLay$

`Create representation` > `Coloring Method=Secondary Structures`

`Drawing Method=NewCartoon` (also happens with `NewRibbons`)
The secondary structure is not shown properly:;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkEf8WjdM$

Below I've copied the text that is printed out in the terminal while
showing the Secondary Structure.

I've investigated the problem, and it is related to Mesa.
I'm running the latest version of Mesa, that being 22.2.3 (dated
Here are the release notes:;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkDh4a7Wb$

If I downgrade to Mesa 22.2.1, the problem still exists.
If I downgrade to Mesa 22.1.7, NewCartoon and NewRibbons Secondary
structure are shown OK.

What is the origin of NewCartoon Secondary structure conflict with the
latest Mesa update?

*Terminal output: *(when using the latest version of Mesa 22.2.3)
$ vmd 6eid.pdb
Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
Info) Email questions and bug reports to
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
Info) Free system memory: 16GB (70%)
Info) No CUDA accelerator devices available.
Info) OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (WHL GT2)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 3 plugins in directory:
Info) /home/david/programs/vmd-1.9.4a57/build/lib/vmd
Info) File loading in progress, please wait.
Info) Using plugin pdb for structure file 6eid.pdb
Info) Using plugin pdb for coordinates from file 6eid.pdb
Info) Determining bond structure from distance search ...
Info) Eliminating bonds duplicated from existing structure...
Info) Finished with coordinate file 6eid.pdb.
Info) Analyzing structure ...
Info) Atoms: 4265
Info) Bonds: 4322
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 568
Info) Waters: 50
Info) Segments: 1
Info) Fragments: 70 Protein: 2 Nucleic: 0
vmd > Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.