VMD-L Mailing List

From: Zilong HE (he-zilong053_at_g.ecc.u-tokyo.ac.jp)
Date: Wed Sep 25 2024 - 04:21:31 CDT

I just found the message from the archive on VMD website, and it appears
that the external link (from http to noupdate=yes, with percent signs
replaced with asterisks) to image attachment has been flagged as unsafe
content. I am not very familiar with mailing lists in general, so apologies
for the troubles :( Maybe I should just have the image from my friend
uploaded as an attachment below.

On Tue, Sep 24, 2024 at 8:22 PM Zilong HE <he-zilong053_at_g.ecc.u-tokyo.ac.jp>
wrote:

> Howdy, VMD users and developers,
>
> In a Windows 10 computer with Intel graphics driver, when
> displaying atoms as spheres with VDW drawing method, the GLSL rendering
> mode in a 32-bit VMD 1.9.3 has been spotted to show two kinds of baffling
> artifacts. Although they only affect visual quality in the graphical window
> and not in the rendered results using e.g. Tachyon, resolving them is
> still good to relieve eye strain a bit.
>
> Under perspective projection, all spheres look very deformed, with at
> least two fragmented surfaces intertwining at different angles. Upscaling
> spheres with the size parameter or zooming in for a close-up look will make
> it worse.
>
> Under orthographic projection, if any material with opacity between 0.5
> and 1.0 is selected like Glass2 and Translucent, and the line of sight is
> not aligned with the z-axis, then some kind of dark shading of atoms occurs
> with noisy, curved, pixelated edges as well as sharp, straight edges. It
> makes a dazzling, strobing visual effect when atoms are rotated. The
> display settings of near clip and far clip seem to interact with the
> shading.
>
> The issues have been posted to another forum as well by a friend of mine
> with a methane as example: [external link to image, note the screenshots in
> (b) and (a), compared with Tachyon rendering in (d) and (c)]
> https://urldefense.com/v3/__http://bbs.keinsci.com/forum.php?mod=attachment&aid=OTgyMDB8NzhjZGNiZmR8MTcyNzE1Mjg4M3w2MDkzN3w0NTg0Mg*3D*3D&noupdate=yes__;JSU!!DZ3fjg!9fZuKesHvGFk0BODqgj4DZpMeVbVWF3W5o2YYvtOIxcjYvyJB-SJefN_4mZGvMLWW9DHdu2vcR2WokYsCVl-mLd2lFPxhlbuIZ8$
> <https://urldefense.com/v3/__http://bbs.keinsci.com/forum.php?mod=attachment&aid=OTgyMDB8NzhjZGNiZmR8MTcyNzE1Mjg4M3w2MDkzN3w0NTg0Mg*3D*3D&noupdate=yes__;JSU!!DZ3fjg!971Xpk8-B3b5YqzfqESdw6HAHODCGsfCUta12GDf3HvQ9DWpijxfHRbh4f29Pljtdu4P4LL7kzA4rqLxSTkUAFJRpfBjcMa31pc$> Neither
> of us have enough knowledge about the inner workings of OpenGL in VMD. If
> it is okay, we would also like to translate and crosspost useful
> information in this discussion to that forum.
>
> Any help is gladly appreciated. Thank you.
>
> Regards,
> Zilong
>


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