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

Oliver Clarke olibclarke at gmail.com
Thu May 19 12:01:53 PDT 2016

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?

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