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| 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 would not be available. | '''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. |
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| If you are running a full EMAN refinement and you wait until it converges, then getting these values is straightforward. Untar the cls.*.tar file from the final iteration. These cls files are the particles associated with each projection (ie - that gives you 2 of the Euler angles). Each line in this file contains a particle number from start.hed, then at the end of the line is: similarity, rotation (radians), dx, dy |
''' ''' '''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 would not be available. If you are running a full EMAN refinement and you wait until it converges, then getting these values is straightforward. Untar the cls.*.tar file from the final iteration. These cls files are the particles associated with each projection (ie - that gives you 2 of the Euler angles). Each line in this file contains a particle number from start.hed, then at the end of the line is: similarity, rotation (radians), dx, dy |
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 would not be available.
If you are running a full EMAN refinement and you wait until it converges, then getting these values is straightforward. Untar the cls.*.tar file from the final iteration. These cls files are the particles associated with each projection (ie - that gives you 2 of the Euler angles). Each line in this file contains a particle number from start.hed, then at the end of the line is: similarity, rotation (radians), dx, dy