VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 11 2017 - 10:00:13 CDT
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Dallas,
If the problem is cured with VMD 1.9.4 that's fine with me. However,
if you see anything unusual with the VMD 1.9.4 code, do let me know.
Best,
John Stone
vmd_at_ks.uiuc.edu
On Wed, Oct 11, 2017 at 09:57:25AM +1100, Dallas Warren wrote:
> Just downloaded 1.9.4a8 and the stuttering is not there now. So the
> it's definitely the bug that you already knew about and fixed.
>
> I only have lights 0 and 1 on, just using the standard settings, I
> have not changed anything with the lighting etc other than the
> commands you noted above. The stuttering that I observe after
> normalising the light sources is within the licorice representation
> itself, the shadows are fine. It appears like the atom sphere appears
> and disappears between frames, or something like that. Not sure if
> you want to pursue further, let me know if you do.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren_at_monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>
> On 11 October 2017 at 08:09, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Dallas,
> > Do you have any other lights on (besides 0 and 1)? All lights that
> > are "on" have to have normalized directions in VMD 1.9.3, otherwise
> > the bug can/will occur.
> >
> > Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Oct 11, 2017 at 07:54:40AM +1100, Dallas Warren wrote:
> >> John,
> >>
> >> Using those light settings with 1.9.3 eliminated the shadow stuttering
> >> and jagged edges in the shadows from the licorice representations. It
> >> did introduce a stutter though in the atom part of the licorice
> >> representation.
> >>
> >> I'll download and install 1.9.4 alpha and see how it goes.
> >> Catch ya,
> >>
> >> Dr. Dallas Warren
> >> Drug Delivery, Disposition and Dynamics
> >> Monash Institute of Pharmaceutical Sciences, Monash University
> >> 381 Royal Parade, Parkville VIC 3052
> >> dallas.warren_at_monash.edu
> >> ---------------------------------
> >> When the only tool you own is a hammer, every problem begins to resemble a nail.
> >>
> >>
> >> On 10 October 2017 at 14:17, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> > Dallas,
> >> > Try running the publicly posted VMD 1.9.4 alpha instead,
> >> > and see if it occurs there or not. I fixed a bug that affected VMD 1.9.3
> >> > where a non-normalized light direction would cause problems in the OptiX
> >> > renderer. You could also do this in VMD 1.9.3 and see if it cures the problem
> >> > (assuming you're just using lights 0 and 1):
> >> > light 0 pos {0 0 1}
> >> > light 1 pos {0.435 0.869 0.217}
> >> >
> >> > Those are both unit-length light directions that should avoid triggering
> >> > the bug that I had in the OptiX renderer in VMD 1.9.3. In VMD 1.9.4 alpha
> >> > and later, the problem is fixed internally and it doesn't matter.
> >> >
> >> > Best,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> >
> >> > On Tue, Oct 10, 2017 at 12:43:57PM +1100, Dallas Warren wrote:
> >> >> Generating a y-axis rotation animation, using Movie Generator with
> >> >> TachyonL-Optix renderer, 2D, standard projection, AO on.
> >> >>
> >> >> Between frames, the shadow generated by the overhead light source with
> >> >> the licorice representation and visible on a QuickSurf representation
> >> >> stutters and has the wrong appearence. It's jaggered at the points
> >> >> where the cylinder for the bond and the sphere for the atom join
> >> >> together in the shadow, almost like it is a low quality polygon rather
> >> >> than high one have used.
> >> >>
> >> >> Currently generating an animation using Internal Tachyon to see if it
> >> >> is there too, but that does take quite a bit longer to generate. Will
> >> >> reply as soon as have some details there.
> >> >>
> >> >> John, can send you a link to a file, privately, to show what is
> >> >> happening if required.
> >> >>
> >> >> Catch ya,
> >> >>
> >> >> Dr. Dallas Warren
> >> >> Drug Delivery, Disposition and Dynamics
> >> >> Monash Institute of Pharmaceutical Sciences, Monash University
> >> >> 381 Royal Parade, Parkville VIC 3052
> >> >> dallas.warren_at_monash.edu
> >> >> ---------------------------------
> >> >> When the only tool you own is a hammer, every problem begins to resemble a nail.
> >> >
> >> > --
> >> > 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/
> >
> > --
> > 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/
-- 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/
- Next message: Prof. Eddie: "Re: Is occulus rift plug-and-play with VMD yet? If so, what are the capabilities?"
- Previous message: John Stone: "Re: Bug report for NAMDgui plugin in VMD (1.9.4 alpha 8)"
- In reply to: Dallas Warren: "Re: Stuttering in video with TachyonL-Optix"
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