PCA App

Issue #253 new
Lars Skjærven created an issue

SEARCH tab

  • Save / load session

ALIGN tab

  • it should be able to extract the sequence identity between structures in other ways than downloading the matrix

FIT tab

  • Import alignment to pymol session.
  • Consider having the occupancy field changed to alignment position so the user could select and display equivalent positions across the ensemble more easily. Do you think will work easily in PyMol also? Or should we leave the original files alone?
  • Option to show ligands (obviously only one structure at the time)?
  • VMD state file ?
  • The heatmap display can suffer when there are lots of structures and having no interactivity or sense of values here is a real shame. See: http://kbroman.org/qtlcharts/example/iplotCorr.html We can do this with some of the JS libs and this would also be cool for other heatmap occurrences.

PCA tab

  • The interactive scree plot needs the cumulative variance as labels for the points (or potentially better as a separate axis in position 4).
  • Initial implementation could be confined to PC1-2 or 1-3 space distances with a letter update to include PCs covering 90% of original variance.
  • We should explore having an interactive alternative so positions can be identified more easily.
  • See previous comments about the DT table (https://bitbucket.org/Grantlab/bio3d/issue/230/pca-app-tab-1-search). The "RMSD cluster" col should be called just "Cluster" or "RMSD/PCA cluster"

NMA tab

  • Conformer plot with arrows ?

Comments (11)

  1. Lars Skjærven reporter

    Note that the SEARCH tab is super slow for entries with many hits. Try e.g. with PDB ID "1CDK". I think we need to do something about that. Is that because of rendering the datatable of 4788 entries?

  2. Shashank Jariwala

    blast_render.R: We are using deferRender = TRUE in renderDataTable. Maybe the bottleneck is somewhere else.

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