[Chimera-users] Display a spider volume data in a specific orientation

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 7 12:30:43 PDT 2010

Hi Zongli,
This is not my area of expertise (our expert is currently out of town)  
-- at first I thought you could use "Transform Molecule  
Coordinates" (under Tools... Movement), but now I see that it works  
only on atomic structures rather than maps:

It only works on molecular structures because it actually changes the  
atomic coordinates, without changing the model transformation.

I've figured out one workaround, but it is both crazy and slightly  
(1) open your map (say as model 0).
(2) open any atomic-resolution structure, it doesn't matter what, and  
open it twice -- now you have three models.  Don't move them  
separately from the map (yet).  Let's say the atomic structures are  
models 1 and 2.
(3) use "Transform Molecule Coordinates" with desired Euler angles and  
shift on one copy of the atomic structure (say model 1).
(4) use the match command to superimpose the other copy of the atomic  
structure on the one that was transformed:
match #2 #1
(the command can use the whole models since they should have exactly  
the same atoms)
(5) use the matrixcopy command to apply the transformation matrix of  
the second copy of the atomic structure to the map:
matrixcopy 2 0

You might think "why do I need two copies of the atomic structure?  
can't I just transform one copy and then use matrixcopy?" ... in fact  
that's what I tried first, but after it didn't work, I realized it was  
because the Transform tool works by changing the coordinate values and  
not the stored matrix of the model.  It is necessary to match the  
second copy to generate a corresponding matrix, and then matrixcopy  
can be used.

I'm CC-ing the chimera-users at cgl.ucsf.edu list in case other Chimera  
users have suggestions. Our expert Tom G should be back next week and  
he might also have ideas.  In general, it's better to send Chimera  
questions to that mailing list instead of just me, because I could be  
away from work or (like now) lacking a good answer!

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:

> Hi Elaine,
> I have a spider volume data (or mrc density map) from which I got a  
> serious 2D projections. I have the Euler angles for each projection.  
> Is there a way in Chimera that I can use those Euler angles to  
> display the 3D spider volume data (or mrc density map) in a specific  
> orientation that corresponding to that 2D projection?
> Thank you very much in advance.
> Best,
> Zongli
> ****************************************
> Zongli Li, Ph.D.
> Howard Hughes Medical Institute
> Department of Cell Biology
> Harvard Medical School
> C Building, Room 420B
> 240 Longwood Avenue
> Boston, MA 02115
> Tel: 617-432-4095 (Office)
>     617-432-4708 (EM Suite)
>     617-432-4091 (Computer room)
> Fax: 617-432-1144
> Email: zongli_li at hms.harvard.edu
> ***************************************

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