Re: [PyMOL] rotate about an abitrary axis

Hi, 

I understood the question a little differently than Andreas, and I have a
different answer to you. 

If what you want to do is to be able to define your own x, y and z axis and
rotate about them, I can help you. I've made a script that will make a
transformation matrix that can be input to transform_selection().  This will
enable you to choose the x, y and z axis yourself, and after you've performed
transform_selection(), you can rotete about your newly defined x, y and z axis
using the rotate command as you would normally do. 

I'm including the script along with an example of a run here, so you can see how
it works. 

Basically, you have to choose three atoms, given with a selection string each,
and these three atoms will form a 2D plane. From the unit vectors the z axis can
also be computed, and thus a transformation matrix can be generated. 

Note that transform_selection() is currently unsupported, so I don't know if
this script will work through newer versions of Pymol. Also, I made this script
purely for myself, so it doesn't contain alot of error checking :) 

Hope this helps! 

Example of usage: 

PyMOL>import coordinateOperations
PyMOL>a =  "r. CLA and i. 612 and n. C1B"
PyMOL>b =  "r. CLA and i. 612 and n. CHA"
PyMOL>c =  "r. CLA and i. 612 and n. C4C"
PyMOL>matrix = coordinateOperations.getTransformationMatrix(a, b, c)
PyMOL>m_list = coordinateOperations.listOfTransformationMatrix(matrix)
PyMOL>cmd.transform_selection("all", m_list)

Cheers, 
Siv

On 2007-06-24 16:07:00, Andreas Henschel wrote:

> you define a rotation axis by the rotation axis x, y or z (first 
> argument in cmd.rotate) and a point in 3d (origin argument in cmd.rotate).
> Instead of rotations around axes that are not parallel to the x, y or z 
> axis you can do composite rotations.
> 
> Btw, for the case of GroEL (PDB 2c7e), the structure is oriented along 
> the Z axis, so you can flap the flexible regions with a single rotation 
> around the axis that goes through the regions center of mass and is 
> parallel to the z-axis.
> See the attached file.
> 
> repeat the last rotate command from the gray window
> cmd.rotate("z", 30, "flexregion", camera=0, origin=rotationCenter)
> 
> Minh Nhat wrote:
> >Hi everyone,
> >Is it possible to make a selection rotate about an arbitrary axis 
> >(which we can actively define ourself (not x,y, z) ?)
> >Thanks,
> >
> >Send instant messages to your online friends 
> >http://uk.messenger.yahoo.com
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> Andreas Henschel
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-- 
Siv Midtun Hollup 
PhD Student
Dept. of Informatics
University of Bergen, Norway
si...@ii... (NOTE: new email adress)
- Blessed are the flexible, for they can be tied into knots. -