VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Aug 29 2015 - 08:47:09 CDT
The first step is to ensure that your structures are aligned.
You should be able to use one of the RMS alignment tools or a short
VMD script to align all of your structures against an original.
To get atom "A" at the same location in all frames, I think the simplest
thing would be to put it at the origin of the coordinate system which
would also be roughly in the center of the field of view. If you do
that for the reference frame, and then align all other frames to
the reference that should ensure that you end up with a trajectory
that is easy to work with for generating a movie. Start out like
this and the rest should be pretty easy and you shouldn't have to
do special scripting for the camera.
On Fri, Aug 28, 2015 at 10:15:22PM -0600, Eric Smoll wrote:
> Hello VMD users,
> I have a series of MD-snapshot pdb files that distribute a specific atom
> "A" throughout a larger molecular system. I am trying to compare these
> snapshots by moving the origin to "A" and rendering the image. I was
> hoping each image would show atom "A" in the same location and with the
> same size. Unfortunately, they do not.
> Reading through the vmd mailing list archive, I found references to the
> rotate, center, scale, and global matrices. I attempted to set a good
> perspective on a representative pdb snapshot, save these matrices, and
> hard code them into my render script. Unfortunately, this does not work as
> I intend either.
> Is there a way to set the VMD camera to a specific location so all
> rendered images draw atom "A" in the same location with the same size?
-- 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/