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

Tom Goddard goddard at cgl.ucsf.edu
Tue Apr 13 11:08:01 PDT 2010

Hi Zongli,

  I've improved the Chimera Transform Molecule Coordinates dialog to 
allow using Euler angles to reorient volume data and other non-molecule 
models.  The dialog has been renamed to "Transform Coordinates" and is 
under the Tools / Movement menu.  You can get this improved version in 
tomorrow's Chimera daily build.

  There are alternate Euler angle conventions.  Chimera only uses the 
chi-convention as described in the Chimera manual:


"Euler angles [? ? ?] - rotations defined by the ?-convention, where the 
first rotation is by an angle ? about the Z-axis, the second is by an 
angle ? (potentially ranging from 0 to ?) about the new X-axis, and the 
third is by an angle ? about the new Z-axis."

  Hope this is the Euler angle convention you are using.


> Thanks a lot, Elaine. I'll try it your way before I got other suggestions.
> Best,
> Zongli
> ________________________________________
> From: Elaine Meng
> Sent: Wednesday, April 07, 2010 3:30 PM
> To: Li, Zongli
> Cc: Chimera BB
> Subject: Re: Display a spider volume data in a specific orientation
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html
>  >
> 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
> tedious:
> (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
> -----
> 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
>> ***************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100413/e1532ed5/attachment.html>

More information about the Chimera-users mailing list