[Chimera-users] defining rotation of a chimera markers file

Thomas Goddard goddard at cgl.ucsf.edu
Wed Jan 24 10:42:59 PST 2007

Hi Jeff,

   Attached is a Python script to rotate Chimera markers about the 
origin using specified Euler angles.  You open the script with Chimera 
menu entry File/Open... to apply the rotation which is specified at the 
end of the script.


Jeff wrote on Wed, Jan 24, 2007:

thanks Tom (and Elaine),

did not have the chance to reply yet. I have not done a whole lot w/ 
Euler angles in general but do know there are several conventions - 
seems like one for each package...

As for a convention, the reason this came up is b/c the slicer tool in 
the IMOD viewer allows the user to rotate the volume according to the 
angles listed in the slider tool window. I use IMOD quite a bit to look 
plane by plane in various orientations in a reconstruction, and I'd like 
to be able to go back and forth with chimera (the IMOD extension in 
chimera only cycles through z; for an arbitrary plane, one would have to 
rotate the volume and reload into chimera). So, the convention used by 
IMOD would be preferred by me, for practical reasons. Here's the manpage 
for 'rotatevol' in IMOD, which mentions the convention:


15 lines of code is fine; I might actually be able to dissect something 
that size and use it to learn. If I had a script I could do it through a 
python prompt, which would get me started. A command in chimera would be 
nicer, but not required (same goes for a graphical interface).

You know, if I knew how to import the marker positions into an array in 
python, I could probably play with this myself - I guess I would also 
have to know how to write out the file too, and I'd have to brush up on 
my rotations. I have scanned through the contents of a marker file (`cat 
foo.cmm | less`, for example) and realize it is text, but I don't have 
enough familiarity with python to parse it into something useful. If you 
were to write a simple script,  for basic I/O of a marker file (or tell 
me how to go about that) and a rotation matrix / execution as an 
example, I could probably run with that. For instance, if I do some 
things in EMAN or SPIDER, I might be able to adjust the convention when 
needed without further assistance. At some point, I'd like to know 
enough to make extensions for chimera, but lack the time to plug away at it.

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