### Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

```Thanks Jared,
I have tried the transformations.py script, and here is what I've got:
- I get a quaternions from external source (a 3d manipulator) in a
classical form: [x,y,z,w]
- I use function: quaternion_matrix(quaternion) from transformations.py
script:

m = quaternion_matrix([x, y, z, w])# m is an array of an arrays (4x4)
M = [m[0,0], m[0,1], m[0,2], m[0,3], m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3], m[3,0], m[3,1], m[3,2], m[3,3]]   # so i
need to convert it to a vector 16x1
cmd.transform_selection(all, M, homogenous=1)  # its time to apply the
vector into a transform_selection function; homogenous=0 also doesn't work
print M # print works fine ;)

But the function transform_selection does not work and I don't really know
why, rotation doesn't occur.
Maybe it's because the selection is wrong? On the scene I have a CGO (an
arrow) and even when I change the selection string from all to arrow it
doesn't rotate either.
What exactly is the selection, could this be a CGO?

I have also noticed, that function cmd.rotate(...) works for my CGO arrow
when I set property object=arrow and I put some arbitrary hardcoded
parameters (axis and angle).
Maybe the better way would be use this function?
But I'm not really sure which function from transformations.py script
should I use to convert quaternions to axis and angle params required by
cmd.rotate() function...
any ideas?

Cheers,
Pawel T.

2015-08-13 18:34 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

Hi Paweł -

Honestly, if you prefer to use matrices, I'd say just go ahead and use
get_object_matrix; I doubt it's going away any time soon.  You may want to
use this in combination with transform_selection
http://www.pymolwiki.org/index.php/Transform_selection.

Also maybe check out Christoph Gohlke's transformations.py script
http://www.pymolwiki.org/index.php/Transformations.  It offers several
tools for manipulating quaternions, matrices, and angle/axis operations.  I
think there's also a newer version on his website, which is linked from the
wiki page.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/

On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski croov...@gmail.com wrote:

Hello,
I've created a CGO in pymol script (a cone) and I need to make some
transformations on it. I've found that it is easier for me to modify a TTT
matrix rather than using translate/rotate functions.

Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix]
get_object_matrix is unsupported operation. So how to get/set TTT?

The problem is, that I get (from external source) position in quaternions
and now I need to make my CGO position equal to those quaternion. How can I
make it work?

Thanks
Paweł Tomaszewski

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### Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

```Hi Paweł -

Honestly, if you prefer to use matrices, I'd say just go ahead and use
get_object_matrix; I doubt it's going away any time soon.  You may want to use
this in combination with
transform_selectionhttp://www.pymolwiki.org/index.php/Transform_selection.

Also maybe check out Christoph Gohlke's transformations.py
scripthttp://www.pymolwiki.org/index.php/Transformations.  It offers several
tools for manipulating quaternions, matrices, and angle/axis operations.  I
think there's also a newer version on his website, which is linked from the
wiki page.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/

On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski
croov...@gmail.commailto:croov...@gmail.com wrote:

Hello,
I've created a CGO in pymol script (a cone) and I need to make some
transformations on it. I've found that it is easier for me to modify a TTT
matrix rather than using translate/rotate functions.

Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix]
get_object_matrix is unsupported operation. So how to get/set TTT?

The problem is, that I get (from external source) position in quaternions and
now I need to make my CGO position equal to those quaternion. How can I make it
work?

Thanks
Paweł Tomaszewski
--
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```