VMD-L Mailing List

From: David Carrasco de Busturia (davidcarrascobustur_at_gmail.com)
Date: Wed Jan 25 2023 - 02:10:51 CST

Thanks. I've tried with the new Mesa 22.3.3 version (dated 1st Jan 2023)
https://urldefense.com/v3/__https://docs.mesa3d.org/relnotes/22.3.3.html__;!!DZ3fjg!45pLP04K75r-fK2boN6zH0rJVMs10eZxB3AocKQ7S5oEuKSIAq2XMA3_tLqP9fksBzswUbQ1hA9p6UaYtK8feF2LeLOa$

The problem still persists.
This time I can no longer downgrade to Mesa 22.1.7 because this breaks
other packages.
Which other graphics drivers do you use with vmd in order to not reproduce
this problem?
Thanks,
David

On Thu, 29 Dec 2022 at 18:17, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I've had another person recently report a similar looking misbehavior
> with similar or the same kind of hardware. I think you've run into a
> Mesa driver bug here, as I don't see this problem with other graphics
> drivers or different hardware.
>
> The disconnected triangles being shown indicate some kind of problem
> with interpretation of mesh connectivity of the triangle vertex arrays
> being drawn. Even in the case that there was some kind of bad secondary
> structure calculation result from STRIDE, the low-level VMD code that
> generates triangle meshes for the NewRibbon and NewCartoon
> representations has been reliable for more than 10 years now.
> Since this issue has only arisen now, I have to conclude that
> these recent Mesa drivers for your hardware are buggy.
>
> If you run the same VMD build on different GPU hardware on the same
> molecular structure, this problem will almost certainly not occur
> (it worked fine for me).
>
> Best,
> John Stone
>
> On Sat, Nov 19, 2022 at 12:48:51PM +0100, David Carrasco de Busturia wrote:
> > Methods `Coloring Method=Secondary Structure`
> > and
> > `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: [1]https://urldefense.com/v3/__https://www.rcsb.org/structure/6EID__;!!DZ3fjg!45pLP04K75r-fK2boN6zH0rJVMs10eZxB3AocKQ7S5oEuKSIAq2XMA3_tLqP9fksBzswUbQ1hA9p6UaYtK8feOhcnhzN$
> >
> > Otherwise, you can also find it here:
> > [2]
> https://urldefense.com/v3/__https://github.com/DavidCdeB/vmd-newcartoon-problem/blob/main/6eid.pdb__;!!DZ3fjg!45pLP04K75r-fK2boN6zH0rJVMs10eZxB3AocKQ7S5oEuKSIAq2XMA3_tLqP9fksBzswUbQ1hA9p6UaYtK8feOkJz_kV$
> >
> > `Create representation` > `Coloring Method=Secondary Structures`
> >
> > `Drawing Method=NewCartoon` (also happens with `NewRibbons`)
> >
> > The secondary structure is not shown properly:
> > [3]
> https://urldefense.com/v3/__https://github.com/DavidCdeB/vmd-newcartoon-problem/blob/main/newcartoon.png__;!!DZ3fjg!45pLP04K75r-fK2boN6zH0rJVMs10eZxB3AocKQ7S5oEuKSIAq2XMA3_tLqP9fksBzswUbQ1hA9p6UaYtK8feIM9paLK$
> > 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
> > 2022-11-07).
> > Here are the release notes:
> > [4]https://urldefense.com/v3/__https://docs.mesa3d.org/relnotes/22.2.3.html__;!!DZ3fjg!45pLP04K75r-fK2boN6zH0rJVMs10eZxB3AocKQ7S5oEuKSIAq2XMA3_tLqP9fksBzswUbQ1hA9p6UaYtK8feCBT6ZLp$
> > 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) [5]http://www.ks.uiuc.edu/Research/vmd/
> >
> > Info) Email questions and bug reports to [6]vmd_at_ks.uiuc.edu
> >
> > 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) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
> >
> > 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/plugins/LINUXAMD64/molfile
> >
> > 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.
> >
> > ```
> >
> > References
> >
> > Visible links
> > 1.
> https://urldefense.com/v3/__https://www.rcsb.org/structure/6EID__;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkAzTKxRX$
> > 2.
> https://urldefense.com/v3/__https://github.com/DavidCdeB/vmd-newcartoon-problem/blob/main/6eid.pdb__;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkP7y3oe7$
> > 3.
> https://urldefense.com/v3/__https://github.com/DavidCdeB/vmd-newcartoon-problem/blob/main/newcartoon.png__;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkMmgW4hF$
> > 4.
> https://urldefense.com/v3/__https://docs.mesa3d.org/relnotes/22.2.3.html__;!!DZ3fjg!4Sffj8MVDR7-A7KzarSaluprfq4FKlwtoXInMtLnEHPFAaEF2-nBUNgQCmb1lUjsiwstw7PNcO_PTTDPYdgjkDh4a7Wb$
> > 5. http://www.ks.uiuc.edu/Research/vmd/
> > 6. mailto:vmd_at_ks.uiuc.edu
>
> --
> Research Affiliate, 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/
> http://www.ks.uiuc.edu/Research/vmd/
>