VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Oct 10 2017 - 17:57:25 CDT

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/