eman1:faq:using_30
Differences
This shows you the differences between two versions of the page.
| eman1:faq:using_30 [2025/07/05 17:53] – created steveludtke | eman1:faq:using_30 [2025/07/05 17:54] (current) – steveludtke | ||
|---|---|---|---|
| Line 16: | Line 16: | ||
| * Monitor the convergence of the overall process by stepping through the iterative 3D models in each directory. When the models in all of the subdirectories seem to have stabilized (don't change much from one iteration to the next), then you can stop (it is possible to run the convergence test in ' | * Monitor the convergence of the overall process by stepping through the iterative 3D models in each directory. When the models in all of the subdirectories seem to have stabilized (don't change much from one iteration to the next), then you can stop (it is possible to run the convergence test in ' | ||
| * When the multirefine has completed and converged reasonably well, we still need to do more. It is very important that you allow multirefine to complete (ie - not killing it in the middle of a run) before this step. The cls*lst files in each subdirectory contain the particles associated with each of the final refined models (except for the first image which is a reference). What we need to do next is combine these images into several new start.hed files and run single model refinements on each of the subpopulations. This will produce much better converged models and will act as an initial validation that the structures you got from multirefine are truly representative of the data: | * When the multirefine has completed and converged reasonably well, we still need to do more. It is very important that you allow multirefine to complete (ie - not killing it in the middle of a run) before this step. The cls*lst files in each subdirectory contain the particles associated with each of the final refined models (except for the first image which is a reference). What we need to do next is combine these images into several new start.hed files and run single model refinements on each of the subpopulations. This will produce much better converged models and will act as an initial validation that the structures you got from multirefine are truly representative of the data: | ||
| - | . mkdir r0 r1 r2 r3 cd 0 foreach i (cls*lst) proc2d $i ../ | + | < |
| + | mkdir r0 r1 r2 r3 | ||
| + | cd 0 | ||
| + | foreach i (cls*lst) | ||
| + | proc2d $i ../ | ||
| + | refine .... (normal refinement) | ||
| + | cd ../1 | ||
| + | foreach i (cls*lst) | ||
| + | proc2d $i ../ | ||
| + | </ | ||
| * Now compare the final refinements in each r? directory. If the data is truly heterogeneous you should see variations characteristic of the variations present in the data. This works very well for things like partial ligand or antibody binding. For things like large-scale dynamics, it also works, but there can be multiple ' | * Now compare the final refinements in each r? directory. If the data is truly heterogeneous you should see variations characteristic of the variations present in the data. This works very well for things like partial ligand or antibody binding. For things like large-scale dynamics, it also works, but there can be multiple ' | ||
| * In general, multirefine will produce a set of models as different from each other as permitted by the data. However, cryoEM data is inherently noisy, meaning if you start with very homogeneous (but noisy) data, you will still get a set of different models out, with the differences being constructed based on variations in the low frequency noise. These variations will generally be fairly small, but the true variations you are looking for could also be small, so you need to be cautious and do some validations | * In general, multirefine will produce a set of models as different from each other as permitted by the data. However, cryoEM data is inherently noisy, meaning if you start with very homogeneous (but noisy) data, you will still get a set of different models out, with the differences being constructed based on variations in the low frequency noise. These variations will generally be fairly small, but the true variations you are looking for could also be small, so you need to be cautious and do some validations | ||
eman1/faq/using_30.txt · Last modified: by steveludtke