VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri Mar 13 2020 - 15:06:39 CDT

Hi Peter,

I'm not sure what you are trying to do, but those matrices should change
the position of the camera, not the coordinates stored in VMD. I believe
that the matricies within viewpoints are meant to be applied to the
center_matrix, rotate_matrix, and scale_matrix accessible through molinfo
(see https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node142.html). Have
you tried something like (operating from memory):

molinfo top set center_matrix {{1 0 0 -119.535} {0 1 0 -144.59} {0 0 1
-132.454} {0 0 0 1}}
molinfo top set rotate_matrix {{-0.409795 -0.495426 0.765888 0} {0.679365
0.394516 0.618708 0} {-0.608684 0.773872 0.174909 0} {0 0 0 1}}
molinfo top set scale_matrix {{0.0305694 0 0 0} {0 0.0305694 0 0} {0 0
0.0305694 0} {0 0 0 1}}

That is what the saved state uses to re-establish the camera positions.

-Josh

On Fri, Mar 13, 2020 at 12:32 PM Peter Mawanga <
peter.mawanga.lagos_at_gmail.com> wrote:

> Hello everyone
>
> From the visualization state, I got the following matrix for changing the
> position of a molecule.
>
> set viewpoints([molinfo top]) {{{1 0 0 -119.535} {0 1 0 -144.59} {0 0 1
> -132.454} {0 0 0 1}} {{-0.409795 -0.495426 0.765888 0} {0.679365 0.394516
> 0.618708 0} {-0.608684 0.773872 0.174909 0} {0 0 0 1}} {{0.0305694 0 0 0}
> {0 0.0305694 0 0} {0 0 0.0305694 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1
> 0} {0 0 0 1}}}
>
> However, after applying the three matrices successively (since the fourth
> matrix is redundant and doesn't make any difference anyway after
> application), all the coordinates were reduced to almost insignificant
> decimal values.
>
> I tried using the "Save coordinates" option to save the molecule position
> after loading the visualization state but it didn't make any difference.
> The "measure fit" command returned an identity matrix too.
>
> Please suggest how to proceed with this issue.
>
> --
> Thanks
> Peter
>