Question: If I have a good template and a bunch of raw particles, is there a way to determine the particle center and orientation by some EMAN programs? In our reconstruction programs, we can get a set of parameters for each particle during refinement again a single reference. Including the x, y shift and 3 angle rotation. We are thinking about getting those parameters from EMAN.
Answer: There are some caveats in this reply. The fundamental refinement strategy in EMAN (1.x) is not really conducive to providing these numbers in a way that they can be reasonably compared to values from another program. While it is possible to produce them, they will not be as accurate as they effectively are during a refinement loop. CTF correction and parameters are taken into account very heavily in a normal EMAN refinement. That is, we have a CTF corrected 3D model, projections are made, then the projections are modified by the CTF before comparison to the raw particles. Unless you pull these parameters out of the middle of a refinement loop, the numbers you get using a straight uncorrected comparison will be less accurate. In addition, one substantial advantage of EMAN refinement is the 2D iterative class-averaging proceedure, which further refines the 2D particle orientations. These numbers are not presently stored anywhere.
If you are running a full EMAN refinement and you wait until it converges, then you can access the approximate orientation parameters produced during particle classification. This is not equivalent to the final refined parameters used to make the class averages, and doesn't include information about which particles were discarded during class-averaging :
- Untar the cls.*.tar file from the final iteration.
- Each cls*lst file (these are readable text files) contains a list of particles related to a particular projection. That is, this gives you the first 2 Euler angles by inference to the proj.hed/img file.
- Each line in this file (after the initial projection reference) contains a particle number from start.hed, then at the end of the line is: similarity, rotation (radians), dx, dy . dx,dy define the center position and the in-plane rotation can be viewed as the third Euler angle.
While the EMAN library does contain conversions between different Euler angle conventions (and there is an even better one in EMAN2), you also have to understand whether each package is rotating the object or the coordinate system, and whether they are doing left or right-handed rotations, etc. Bottom line is that it can take quite a bit of effort to put together a scheme for extracting this information for use in another package and getting all of the details right.
Note that in EMAN2, we will be making this process a lot easier, but that isn't likely to be usable for this purpose before early 2009.