I am trying to generate a reconstruction of my protein using the alignments from a local refinement job and the original particles. However, when I do this I still get the masked volume as an output.
I have used the Homogeneous Reconstruction Only job type. The 3D particle alignments come from a local refinement job, and the particles are those used as the input for the particle refinement job (particle subset job). Below are the input parameters.
I have tried using the particle stack from the local refinement job and replacing the blob file with that of the original particles and got identical results.
Hi Sarah - when you say you want to use the original particles, as opposed to the ones used in local refinement, what is the difference between the two sets? Were the particle images modified in some way, e.g by subtraction? Because otherwise I would expect the reconstruction to look the same as the local (as you are using the same alignment parameters).
Also, the output of local refinement should not be masked I think - a mask is used in refinement, but not applied to the output volume. It may look masked though, as the alignments will be a lot more accurate inside the mask, blurring out the density outside of it.
