I’m really happy with the improving ergonomics and flow of v4. I have a few humble suggestions for more quick actions and a couple of features involving masks:
1) Build 2D classification from each class of a heterogeneous refinement or ab initio job: At early stages of data processing, it is useful to assess the contents of heterogeneous refinements and ab initio using 2D classification, as the volume outputs in 3D can be very misleading.
2) Build local refinements from each class of a 3D classification job: I often use masks in my workflows of large molecules and this feature is notably lacking.
3) Build homogeneous/NU/local refinements from each cluster of a 3DVA display job: I use 3DVA and clustering to deal with continuous heterogeneity in large molecules when I am looking for discrete substructure and/or attempting to build a high-resolution consensus map/model. I typically assess the outputs of clustering with refinements, most often local refinements using the same mask used for 3DVA.
4) Build 3DVA Display along each mode: It might be nice to add a quick action for 3DVA Display for each corresponding mode of a 3DVA job. I often analyze them independently for simplicity.
5) Add feature for creating and applying “Mask Bundles”: I would like to float the idea of creating “mask bundles” where groups of local refinement masks that are consistently used to improve features of a large molecule can be bundled and applied recursively to jobs. For example, I work on a C4 symmetric large ion channel for which I use the same set of 10 local refinement masks to produce high-quality composite maps. This ion channel also exhibits at least four major global conformations, which means that in a single dataset I am often creating 40 local refinements to assess the endpoints of classification, nevermind the intermediate stages of analysis. It would save me tons of clicking if there was a way to take a single consensus refinement (whether homo/NU-refined or symmetry relaxed through expansion and local refinement) and apply local refinements using each mask in a mask bundle. The same could be said for 3DVA. As it stands now, the “Quick Actions” come close to this idea, but I don’t see a way to attach a bundle of masks to the quick actions.
6) BUG: Build Volume Tools from Import 3D Volume job does not build multiple when the Import 3D Volume job contains multiple volumes: Along the lines of above, when producing local refinement masks, I create synthetic density from models and import them en masse using Import 3D Volume job. Currently, if you use the “Quick Action” to build Volume Tools, it only builds a single job using the first imported volume. It would be great if Volume Tools could be applied en masse to all of the linked volumes, since I use the same mask parameters for all of my local masks. Or, at least build a single Volume Tools job for each imported volume.
7) Mask from model: The ultimate fix to 5+6 would be to have a job that can build masks directly from models using residue selections. Bonus points if the job automatically fits the model into the density. Building masks directly from models is the most precise and reproducible method in my hands.
I’m sure you are already thinking about this, but it would be great if there was a “Meta-Job Builder” that allowed us to configure custom “Quick Actions” for certain jobs by using iterables for inputs, for instance every class of 3D classification, every mode of 3D variability display, every volume of import 3D volumes, or every mask of a mask bundle.
Sorry if any of this has already been reported or requested. Without any of the above, v4 is a major improvement in ergonomics/flow and my wrists and eyes thank you! Fantastic!