[Chimera-users] How to convert Coot rotation matrix to something Chimera can read?

Oliver Clarke olibclarke at gmail.com
Thu May 19 12:23:54 PDT 2016

Actually nevermind, I think I have it - something like this seems to work:

~sel; matrixset ~/Desktop/test_matrix.txt; cofr x,y,z coordinatesystem #0;
ac mc; centersel; symclip 5

where test_matrix.txt is the rotation matrix from coot view_matrix(), x,y,z
are the coords of the rotation center from coot, centersel is an  alias
that centers the view on the selection, and symclip is an alias that slabs
around the cofr.


On Thu, May 19, 2016 at 3:01 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all,
> I'd like to write a little python function in coot to open the current
> view with Chimera, because manually replicating in Chimera views that were
> identified in Coot is a little painful.
> The file handling aspects of this seem straightforward - the one aspect I
> haven't quite got yet is how to set the view in Chimera to match that seen
> in Coot.
> I would like to load up all molecules/maps that are displayed in coot, in
> their default orientations, and then apply the view matrix from coot using
> matrixset to get the equivalent view.
> Coot outputs a 3X3 rotation matrix which seems to be the same as that
> generated for an equivalent view by matrixget in Chimera, except that in
> Chimera the matrix is 3X4, with the last column representing the
> translation vector.
> This I cannot access directly within coot, but I can probably calculate it
> if I know what it represents. This is probably a stupid question, but is
> this simply the vector from the origin to the current center of rotation?
> Or is it something else?
> Cheers,
> Oliver.
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