RnallViewer User Guide

The parts

The main window of RnallViewer has four main sections. Below is a picture to use for reference. It does not show all the functionality, but shows the general layout. This page describes their basic functionality. Navigate using the links above or below to get more details about each section.

Gene Annotation and Sequence Viewer

The top lists information about the annotation file -- name, start and stop position, entries, and a current scan section of the sequence file. On the top row, the name, number of proteins and start and stop locations come from the current annotation file loaded. RnallViewer understands protein table format (.ptt) and gbk. Below this is a sequence viewer, which displays and lets you save a specific subregion of the fna file. Hitting the <- and -> buttons will scan back and forward one position, preserving the scan size. Type in a start and stop position and hit rescan to display a specific subregion. Hit save to save the subsection.

Main Display

Below this is the 2D display, where genes and directions are drawn, below which are the energies of structures generated by Rnall. To the right lets you focus on a particular color with given spread and brightness variables, all set by the scroll bars. When you mouse over energies and genes in the display it shows some basic information.

The black lines indicate the "sequence path" and reads like a book. At the top-left is the start position being displayed (7395 in the example picture), and at the bottom right is the last position being displayed (8315 in the example picture). It snakes between them going left to right, then moving down to the next row (see display customization). When you mouse over a structure it displays the energy, window size, and location of that structure. When you select it, that information gets piped to Rnall again where the pipeline takes over (see tools section below).

Tool Controls and Output

Farther down are three fields. The left two are for some textual feedback -- the top has a simple hyperlink navigation system to go through screens showing the results of running some background executables -- for example, the CT file shown in the picture. The bottom left field shows some more low-level interaction -- the actual system calls used and any messages received back.

To the right is where the result of a call to ghostscript will go -- an image pops up corresponding to the CT file.

Finally, at the bottom are some analysis tools. You can set or append structures using the output file from Rnall, which in turn has input based on a variable region chosen from the second pop-up. Alternately you can use an external file. You can manually set the window sizes and energy cut-off level (if the structure's energy is above the cutoff, no CT file and thus no image file is generated). Below this lets you interact more directly with the conversion process from CT file to image file.

3D Display

Anytime you have a section displayed on the main display you can go to Display->Energies Viewer and the 3D energies viewer window will pop up. This is essentially a 3D representation of the Main Display energy data, and selection and highlighting here has a 1-1 correspondence with the 2D main display.