Matthias,
fetch 1cll 1ggz, async=0
print cmd.get_object_matrix("1cll")
print cmd.get_object_matrix("1ggz")
super 1cll, 1ggz
print cmd.get_object_matrix("1cll")
print cmd.get_object_matrix("1ggz")
As you can see when an object is loaded it's transformation matrix is
the identity. Then, when you call "super" is moves the "mobile"
protein by the transformation matrix. Notice the matrix is a 4x4
which means it's:
[ A b ]
where A is the 3x3 rotation matrix, and b is the 3x1 translation vector.
See also: http://pymolwiki.org/index.php/Get_object_matrix
Hope this helps,
-- J
On Mon, Jan 18, 2010 at 5:35 AM, Matthias Haffke
<matze_haf...@hotmail.com> wrote:
> Hi everybody!
>
> I was wondering if there is a way to get a translation / rotation matrix out
> of the "super" command.
> My problem is, that I want to superimpose 2 proteins (lets say protein B
> superimposed on protein A), but I also want to use the same superposition
> (e.g. the same translation and the rotation function / matrix) for every
> symmetry mate of protein B. Is there a way to "extract" the translation /
> rotation matrix out of the super command or can I use another command to
> align both, protein B and A and to apply the function on every symmetry
> mate?
>
> Both proteins don't have to be aligned perfectly, it's much more important
> for me to keep the symmetry operations of protein B. I already tried to use
> the "translate" function to get a sort of alignment (which could then be
> applied to all symmetry mates), but I wasn't very successful. Looks like the
> translate function works in respect of your viewing point but not in respect
> of the cell axis?!?
>
> Matthias
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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