From: John Stone (
Date: Tue Oct 02 2012 - 14:55:31 CDT

  I have some answers to your questions:

On Tue, Oct 02, 2012 at 02:00:54PM -0400, Derya Meral wrote:
> Hi,
> I'm trying to make a high res movie of a trajectory. I am running into
> several problems:
> 1 - I have created 3 representations (1st one colors all proteins based on
> index, 2nd and 3rd representations color specific residues) that I want to
> be superimposed in the final movie, however whenever I try any Renderer
> option other than the Snapshot (Screen Capture), I only see the first
> representation (so the individual residue colors I picked do not show up).
> How can I deal with this issue?

This is likely caused by overlapping representations. When you render
with OpenGL, sometimes you can get away with having two representations
that are mathematically overlapping each other, and in cases where
they're occupying the same space, it will happen to show them according
to their order. When making images with a ray tracer such as Tachyon,
this will not occur, and so you may not see any but one of the reps.
To prevent this, you should use more detailed atom selections to
prevent there from being any overlapping atoms among the different
representations. If you don't want to do that, then another quick
tweak you can do is to increase the radius of the representation that
you want to ensure shows up "on top" so to speak, and that should
alleviate the issue. It is better to use appropriate atom selections,
as this also reduces the amount of rendering work that VMD and any
of the renderers (like Tachyon, POV-Ray, etc.) have to do.

> 2 - Using the VMD movie generator with combinations of options such as
> Internal Tachyon/Tachyon, Trajectory, Animated GIF/MPEG-1/MPEG-2, I'm
> getting very low resolution movies. I have decided that it might be better
> to get the ppm files and perhaps use mencoder to do the movie separately.
> However, I'd still like to know if I'm getting low res movies from VMD
> because of something that I'm overlooking. Is there a way to change the
> resolution of the movie in the movie generator?

The movie resolution will be related to the resolution of your VMD window,
and the movie format you have selected. At most, the final movie would
be 640x480 resolution due to the practical bitrate limitations with the
movie formats supported by the older revs of mencoder and similar tools
that are supported by the built-in options in the movie maker.

That said, you can definitely have the VMD movie maker save the frames
and run your own custom movie encoding commands. We have done this
for our own movies, all the way up to 4096x2400 resolution, although
few movie players for PowerPoint etc will accept files that go beyond
DVD resolution. If you don't care about PowerPoint playback, or you
have a player that works well, then you should be able to do
1080p HD resolutions with no problem using mencoder yourself.

> 3 - I am also unable to change the length of the movie for trajectories,
> except for the 24, 25 and 30 fps options. Is there any way that the final
> movie could be slowed down further other than duplicating images?
> Thank you.
> Derya Meral

The movie maker plays exactly one trajectory timestep per movie frame.
You could address this by duplicating your trajectory frames or by loading
the output images into a movie encoder that will do frame-duplication

  John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349       Fax: 217-244-6078