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Importing 3D Maps from the PDB

There has arisen an issue concerning importing from pdb, transformation to the Brix format, and the rotations that chimera performs relative to this format. We will describe the relationships between the transformations applied within SPARX to the transformations performed in Chimera.

Facts to help sort out the motivation of Phil's struggle on the transformation When dealing with fitting crystal piece into HRS density map:

Capturing the matrices that represent the current state

If, say, a Spider file is opened in Chimera, and the show command from the model panel is used, then Chimera will record the transformations that are performed manually with the mouse using a command such as > matrixget R from the Chimera command line which writes the current transformation, from the point at which the 3D map was opened, to the current state. (The transformation, R, can be reused later in a command such as >matrixset R )

The transformation R is written to a file and can be viewed. The question is

Solution method (Summer 2005)

To go back and forth from the SPARX (`psi_S,theta_S, phi_S `)convention and what Chimera records( `psi_C, theta_C, phi_C` ):

1. I took the tripod, saved to BRIX, and loaded into Chimera

2. Noting the original positions of the tripods legs,

3. For each of these rotations, a, I noted the transformation recorded in Chimera as b.


for each of the rotations, a, with `R_alpha` and `R_beta` unknown but fixed.

The general solution to these sort of problems is not so easy.

But in this particular case, the problem is not quite so hard and I found (with a certain amount of guesswork):

Notice that `R_beta`is its own inverse `R_beta = R_beta^(-1)` . So a = `R_beta` b `R_beta` and b = `R_beta` a `R_beta`