Differences

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--- eman2:e2tomosmall [2025/08/05 10:29] – [New Initial Model Generator] steveludtke
+++ eman2:e2tomosmall [2025/08/05 11:06] (current) – [Particle extraction (~2 min (a few manual) - hours (a couple of thousand))] steveludtke
@@ Line 284: / Line 284: @@
   * If you did the previous optional annotation step above, you will be able to see the selected particles here, and if you like, manually update them.
-===== Particle extraction (~2 min (a few manual) - hours (a couple of thousand)) =====
+===== Particle extraction (~2 min (a few manual) - over an hour (a couple of thousand, large tutorial)) =====
 Note that this step will be vastly different resource-wise if you are only extracting a few manually selected particles for purposes of later template matching or if you already selected hundreds of particles from each tomogram.
+<note>
+Depending on how you selected particles you may have a significant number of particles which contain fiducials or artifacts from the fiducials (bright spots). Having these in your particle data can cause significant problems, and could lead to getting bad initial models and thus bad refinements. For a small data set like this, it might be a good idea to open the manual boxer for each tomogram and delete any particles with fiducials in them before completing this step (particle extraction).
+</note>
 The reduced 1k x 1k (or 2k) tomograms are used only as a reference to identify the location of the objects to be averaged. Now that we have particle locations, the software returns to the original tilt-series, extracts a per-particle tilt-series, and reconstructs each particle in 3-D independently at full resolution. Since this is performing a full resolution reconstruction of each particle it is somewhat resource intensive.