KnownLimitations
Due to limitations on our testing hardware, we are only able to officially support the most recent releases of Mac OSX (curently >= 10.14). Please post a new issue if you experience installation problems running OSX 10.12 or higher (versions still supported by Apple) and we will try to help.
The main window launched when the application is first run does not resize. In our tests allowing variable resizing of this window can lead to unpredictable display results. If you run into any issues with the main window clipping scrollbars or other essential parts of the screen that you need for usage of the program, please contact us over email or file a new support issue request!
The maximum subsequence length highlighted by the radial layout viewer (SHIFT+R from the Diagram Window) is limited to <= 500 bases. Figures that involve substantially more bases than 500 tend to display poorly in our tests. Try to select a smaller region in the zoom window to focus on.
Only a maximum of 20 samples may be contained in any single file in the Boltzmann file format. This decision has been made to limit potential crashes and system memory issues that may arise in the typical use case of this file format where thousands of samples are generated per file.
See the FAQ entry about this limitation for a proposed solution.
The resolution of the zoom subwindow found in the diagram window (see below) is low resolution by design. This design choice allows the user to zoom in on a particular segment (range) of base indices around the circle in the diagram window display, which can then be combined with SHIFT+G or SHIFT+R to open either a CT file viewer window focused on that base pair range, OR a radial display viewer of the structure highlighting that base pair range. The low resolution display of the zoom subwindow optimizes the running time spent by successive zoom operations.
RNAStructViz will not load duplicate FILES (e.g., files on disk with the same basename), but it will by default load duplicate structures. If you do not want the application to load duplicate STRUCTURES even though they are specified in different FILES, then you can check the highlighted (circled in red) checkbox in the "Load Files" dialog shown below:
There are known rounding issues that happen when trying to place the ends of the base pair arcs in the arc diagram viewer in precisely the expected location around the bounding circle. It also clutters the display, and hence makes the diagrams less reusable, to have too many tick markers around the bounding circle in these diagrams. Thus we settle for a middle ground and place approximately 12 evenly spaced tick markers around the bounding circle (see example below). This design decision somewhat limits the ability to obtain fine-grained information about the pair base position locations from the arc diagram viewer. To see exact base pairing specifications for the structures displayed in these diagram types, use the CT-style file viewer, which can be launched from the arc diagram window on a zoomed region by pressing the key combination of <CTRL+G>.
In the following example, we use the variant of the O. nivara structure referenced in issue #85 to demonstrate how the precise base index positions can be muddled by taking a singular view of only looking at the arc diagram window in RNAStructViz:
The CT viewer perspective, on the other hand, gives a less coarse view of the overlapping arc trends we are seeing above:
