VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 11 2021 - 16:29:09 CST

Hi,
  It sounds to me like you're experiencing an issue with the behavior
of the graphics drivers on Ubuntu. What do the VMD startup messages
say in the text console when it first starts? I'm particularly interested
in the messages associated with the OpenGL renderer. If you have a buggy
OpenGL driver, then you may want/need to use one of the other rendering
approaches such as TachyonInternal instead of snapshot.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jan 10, 2021 at 10:17:35AM +0000, Arham Amouie wrote:
> Hello
> I use VMD 1.9.3 on Kubuntu 20.04 on a rather old laptop. I'm trying to
> make a simple animation from hundreds of xyz files produced with a
> simulation. Here is the script for rendering the frames:
> display resize 389 343
> display nearclip set 0.001
> set indir "in/"
> set outdir "images/"
> for {set filenum 0} {$filenum <= 692} {incr filenum 1} {
> mol new [format "%s%05d.xyz" $indir $filenum] type {xyz} first 0 last
> -1 step 1 waitfor -1
> molinfo top set {center_matrix rotate_matrix scale_matrix
> global_matrix} {{{1 0 0 -885.859} {0 1 0 -750.065} {0 0 1 -750.047} {0 0 0
> 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.00180681 0 0 0} {0
> 0.00180681 0 0} {0 0 0.00180681 0} {0 0 0 1}} {{1 0 0 0.78} {0 1 0 0.05}
> {0 0 1 0} {0 0 0 1}}}
> rotate x by $filenum
>
> mol modstyle 0 top Points 1.000000
> render snapshot [format "%s%05d.tga" $outdir $filenum]
> mol delete top
> }
> Each xyz file contains ~1.5 million atoms and I'm sure that the xyz files
> are not corrupted.
> Now, the problem is that some of the rendered images are irrelevent/wrong.
> For example, some of the saved frames show a black screen with VMD logo on
> it. I also used 'display update' and 'sleep 2' before the render command,
> but they didn't help.
> Kind regards,
> Arham Amouei 

-- 
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/