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Hi Zongli,<br>
<br>
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.<br>
<br>
There are alternate Euler angle conventions. Chimera only uses the
chi-convention as described in the Chimera manual:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/transform.html">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/transform.html</a><br>
<br>
"Euler angles [φ θ ψ] - rotations defined by the χ-convention, where
the first rotation is by an angle φ about the Z-axis, the second is by
an angle θ (potentially ranging from 0 to π) about the new X-axis, and
the third is by an angle ψ about the new Z-axis."<br>
<br>
Hope this is the Euler angle convention you are using.<br>
<br>
Tom<br>
<br>
<br>
<br>
<br>
<blockquote
cite="mid:EC6FF3857AF8CE4AAB49A278A59832ACA0AC4839D4@ITCCRMAIL01.MED.HARVARD.EDU"
type="cite">
<pre wrap="">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:
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html"><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html
></a>
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 <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> 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:
</pre>
<blockquote type="cite">
<pre wrap="">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
***************************************
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