Enhanced Pathfinding

Important: paths generated with the previous generation will not transfer to the new one. Although you can still open them, the paths will look nothing like before and will need to be deleted and re-calculated. Prolines were also misbehaving slightly; existing RoPE directories will benefit from a run of "Refine all" from the entity menu.

This is a pretty large update.

Features

• Paths have changed significantly (beta feature!):
  • Each calculation of a path is now different. This is randomly seeded by shuffling the order of refinement of the individual bonds. This allows the potential path landscape to be sampled. The path generation can be set to save and auto-restart in order to generate a group.
  • The path calculation is now more robust by running the calculation on improving atom-atom pair distances rather than single-atom trajectories, which also improves the treatment of large motions e.g. full domain swings. The distance threshold can be tuned.
  • The path calculation now uses sine waves instead of a polynomial to naturally match the circular nature of torsion angle changes.
  • After refinement of the backbone, side chain torsion angles are refined to minimise the Lennard-Jones potential between nearby atoms, to better treat Van der Waals contacts. The contact distance threshold can be tuned.
  • Better choice of torsion angle flips has been implemented. Occasionally "protein pirouettes" still occur, and for this reason there is an option to increase the number of combination flip trials that will be carried out to remove them. (default 0)
  • The linearity ratio has been removed as it turned out to be misleading, and has been replaced by the Van der Waals energy activation barrier, which is more meaningful.
  • Rudimentary support for clustering on all pathways of the same type (i.e. sets of paths which all start and end at the same protein instances).
• Tabulated data view within the software, particularly useful for metadata so you can see what you're working with. This also allows you to sort by the values of a particular column and export the reordered table as a CSV.
• The axis explorer has been provided with a few new features, some of which are accessible from a new menu in the top right:
  • the calculation of torsion hotspots has been tweaked, and the table corresponding to the tweaks has been made available. These are calculated as the square root of the sum of the squares of torsion angles spanning the main chain associated with each residue ID.
  • you can export a PDB file at a particular point on the slider.
  • axis limits can be temporarily changed from the default of -1 to +1.
  • hover over an atom to read its description.
• better treatment of hydrogens. Hydrogenated and non-hydrogenated PDB files now produce identical torsion angles. This was previously not the case due to hydrogens being included in the initial alignment process. The RoPE space also now discards torsion angles featuring hydrogen atoms, which means there is no systematic separation between PDB files with hydrogen torsion angle-data and those without.

Bug fixes/minor points

• prolines were misbehaving; existing RoPE directories will benefit from a run of "Refine all" from the entity menu.
• clustering on normalised B factors is now available (beta)
• Ctrl+V (on native apps, Linux and Mac) will allow you to paste into RoPE, making many things easier to transfer.
• Non-ASCII characters may not display, but they will no longer cause a crash.
• depth cueing is now available on protein displays. The slabbing can be altered using keys D/F, following the coot convention.
• all sorts of small improvements to the GUI.

Pathfinding

This is a major update consisting of several new features:

Features

• Introduction of pathfinding (beta feature). A putative smooth path can now be calculated and refined between two molecules, using perfect bond length and angle geometry.
• Calculation of distances between different protein entities, accessible through right click on the entity menu (beta feature), expanding the kinds of distances that can be measured and added to metadata.
• The axis explorer now offers to show the associated change of atom positions, to visualise small motions associated with a given vector in RoPE space.
• Rudimentary support for nucleic acids

Bug fixes/minor points

• Bug fix for hydrogen atoms behaving incorrectly during refinement/display
• Small GUI tweaks

Burning protein glow

This is a minor update to tackle some important stability issues.

Features

• In the axis explorer, protein chain glows to show torsion angle motion hotspots, making them easier to spot.
• Window is now fully resizeable and optionally fullscreen in Mac OS X.
• By popular demand, the Escape key asks if you're sure you want to quit instead of immediately quitting.

Bug fixes/minor points

• No more soft lock when you ask RoPE to refine zero models.
• Eliminated a crash introduced in the previous version when exploring the axis of a protein with ligands.

Mouse selection and cluster history

Features

• One can now select models by shift-clicking and dragging a selection window. Alt-click and drag to remove from the current selection. Right click in space to select the group or its inverse to create a new cluster using only these structures.
• Cluster history is now preserved during the course of the RoPE app lifetime and displayed in a tree-style list on the side of the conformational space. Right click a cluster to set a categorical custom metadata tag.
• MacOS app now loads full-screen using the native “Spaces” so the bottom isn’t cut off by the Dock.
• Histidine can now be automatically swapped by 180 degrees to match other instances of the entity in “fix issues”, which is not enabled by default.
• Web version supports high DPI screens.
• When downloading metadata from PDB, the title is retrieved and displayed in the model details.

Bug fixes/minor points

• Model management logic improved.
• Fixed a bug preventing a sequence being loaded from a Fasta file.
• Made the atom menu in the atom-distance-calculator smaller.
• Fixed and clarified several warnings and error messages
• Fixed frequent crashes in Web application
• Small bug fixes and UI improvements throughout the software.

Forced ring closure for proline residues

Features

• Side chains are included in the RoPE space calculation, and displayed on axis explorer (but not part of the legend).
• Prolines are now forced to close properly. If you have ’naughty prolines’ from a previous version which did not force ring closure, you will be prompted to refine your structures.
• Using the “refine all” function in Entity (rather than the run-through via “rope space”) will refine more thoroughly than before. This will use a more intensive refinement protocol following the initial quick refinement. This can drop the target function by over 10% and tighten the SVD axis calculations. This is also the default for individual model refinement.
• [Desktop app only] No need to restart the program in order to load in your own files: simply go to the FileView and click the ‘refresh’ button, which will sync with the local directory. Warnings will be given before PDB files which have been deleted, but are still referenced in a model.

Bug fixes/minor points

• Fixed where viewing global metadata would cause RoPE to crash soon after.
• Fixed where viewing files would only show a subset of files after viewing a PDB.
• Small bug fixes and improvements throughout the code.

Baseline analysis after referee report guidance

Following referee report suggestions and guidance, a new version of the software has been generated which addresses several aspects of the algorithm among other good changes.

Reorient axes according to colour scheme

Features

• Reorient one of the axes according to the displayed colour scheme. Right click an axis and click 'match colour'.
• Chain IDs are now automatically grabbed metadata when creating an instance of an entity.
• It is possible to hide an origin again without pressing 'back' in RoPE space. Right click empty space and then click 'hide origin'.

Bug fixes

• Some severe GUI-crashing bugs have been fixed.
• Custom amino acid display now maps onto the reference sequence to ensure correct amino acids are highlighted.

Baseline RoPE analysis

RoPE analysis - code baseline for generating RoPE space from protein structures.