VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 23 2021 - 13:52:41 CDT

Hi,
  Aside from what others have mentioned, a concern with transparent
or reflective geometry is whether you have a case where two surfaces
exactly overlap each other. In the real world you can't have two things
occupying the same space, but in a tool like VMD you can create cases
where surfaces are either unintentionally duplicated (e.g. two of the same
representation) or where they happen to coincide with some perfectly overlapping
triangles. This can cause a huge drop in performance and/or deadlock if
multiple transparent surfaces overlap in just the right way, particularly
if you're very near the limits of floating point precision for the ray-surface
intersection calculations required. I would suggest checking to see if you
have any duplicated or nearly-exact overlapping transparent surfaces,
and try to eliminate them.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 23, 2021 at 05:44:15PM +0000, Jason Smith wrote:
> Hi Prateek,
>
> I remember having trouble (on windows) with something similar.
> Transparency would cause a hang because most of my ram and vram was
> actually busy with another program - turning off transparency would work
> fine though, as did turning off the other programs like web browsers.
> However, I also know there have been some Mac specific problems in the
> past. Perhaps try to see if memory or OS is a contributing factor?
>
> Cheers,
>
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> --------------------------------------------------------------------------
>
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Vermaas, Josh <vermaasj_at_msu.edu>
> Sent: Monday, 23 August 2021 9:47 AM
> To: Prateek Bansal; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: VMD Tachyon Render fails with new material
>
>
> Does it "work" with one of the glasses? Transparent surfaces make Tachyon
> do *a lot* more work. Depending on your settings, it can take quite a
> while to render, especially with CPUs only, like it would be on a Mac.
>
>
>
> -Josh
>
>
>
> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Prateek Bansal
> <bansalprateek97_at_gmail.com>
> Date: Monday, August 23, 2021 at 12:26 PM
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: VMD Tachyon Render fails with new material
>
>
>
> Hello VMD Community,
>
>
>
> I am trying to use VMD to visualize a membrane protein. I have output from
> the HOLE2 program which lets me visualize the tunnel inside it. To
> visualize the tunnel better, I use a surf representation of the protein
> and make a new material with lesser opacity. When I try to render it using
> Tachyon/Tachyon Internal, VMD stops responding and I have to end up
> closing it. Rendering works when the material is one of the default ones
> (Opaque, for e.g.). Any insights would be appreciated.
>
>
>
> I am using MacOS 10.15 (Catalina) and VMD 1.9.4a51.
>
>
>
> Prateek 

-- 
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/