[Chimera-users] matrices

Dougherty, Matthew T matthewd at bcm.edu
Mon Sep 26 10:52:09 PDT 2011

Hi Tom,

can you send me the session?  Having difficulty understanding what you did.  I thought I did the same.
When I create a inverted matrix -1[000] and read it in using a matrixset command, it immediately transforms it to a 2[001] matrix, that is it it creates a positive one for z.

What I would expect for a m[001] matrix interpolating from an identity matrix using a reset command of 100 frames is the object would flatten out or scale from 1 to 0 on the z axis from frames 1-50, and invert 50-100, returning to full scale, but inverted at frame 100.

I should be able to do this in Blender, but would rather do it in Chimera.


Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
From: Tom Goddard [goddard at sonic.net]
Sent: Monday, September 26, 2011 12:36 PM
To: Dougherty, Matthew T
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] matrices

Hi Matt,

   You can use an inversion or inversion combined with a rotation in
Chimera and at least some things work correctly.  I tried the matrixset
command to apply an inversion and the inverted molecule displayed and
rotated correctly, and then I created a surface for the inverted
molecule which worked.  When I then tried to align the inverted molecule
to a copy of the original uninverted molecule, it inverted it back to
give perfect alignment (didn't just do the best pure rotation).

   As far as I know, no thought has gone into making sure Chimera works
with inverted spatial transformations, so some operations with inverted
models may misbehave and you'll have to test and see.


Dougherty, Matthew T wrote:
> I was doing something with crystallographic point group matrices.
> Does Chimera allow for improper rotations and inversions?
> Or does it rectify them as proper rotations?
> I would like to go from
> Model 0.0
>       1 0 0 0
>       0 1 0 0
>       0 0 1 0
> TO
> Model 0.0
>       -1  0  0  0
>        0 -1  0  0
>        0  0 -1  0
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine

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