VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jun 18 2009 - 15:15:34 CDT

You could map the coordinates using the "set" command. You would
need to, e.g., load the molecule twice, changing the coordinates of
one based on the other. It would approximately work like this:

set sel [atomselect 0 all]

foreach ind [$sel get index] {
   set temp1 [atomselect 0 "index $ind"]
   set temp2 [atomselect 1 "index $ind"]
   $temp2 set x [expr -0.79814*([$temp1 get x]-99.4985) + -0.50649*
([$temp1 get y]-55.308) + 0.32625*([$temp1 get z]-26.91025)]
   $temp2 set y [expr ....]
   $temp2 set z [expr ....]
   $temp1 delete
   $temp2 delete
}

You could also do the mapping in place (only loading one structure)
by using intermediate variables for the new coordinates before
setting them.

The 4x4 transformation matrix you are using is composed of a 3x3
rotation matrix and a translation vector (with the last row being as
you have given it), so it might take some work to determine it for
the transformation you want.

On Jun 18, 2009, at 2:55 AM, Thomas Evangelidis wrote:

> Dear VMD users,
>
> I have the new coordinates of a protein in the following form:
>
> X2 = -0.79814*(X1-99.4985) + -0.50649*(Y1-55.308) +
> -0.32625*(Z1-26.91025)
> Y2 = 0.40972*(X1-99.4985) + -0.85333*(Y1-55.308) + 0.32243*
> (Z1-26.91025)
> Z2 = -0.44171*(X1-99.4985) + 0.12367*(Y1-55.308) + 0.88859*
> (Z1-26.91025)
>
> So I set the following matrix for the transformation:
>
> {{-0.79814 -0.50649 -0.32625 -99.4985} {0.40972 -0.85333 0.32243
> -55.308} {-0.44171 0.12367 0.88859 -26.91025} {0.0 0.0 0.0 1.0}}
>
> but the molecule is moved to a completely different location than
> the one it should be. I am confused, either the matrix or the
> coordinates are wrong. Can anyone shed some light on this please?
>
> thanks in advance,
> Tom