### REDCAT Documentation Table of Contents

# The REDCAT menu items

## File

### Prepare Input

Opens the dialog box that creates a REDCAT file from PDB file. For more information see the Prepare Input section of the Main Gui page of this website.

### Import RDC Tool

- Two Column ASCII
- Two Column SPARKY
- RDC from REDCAT
#### RDC from REDCRAFT

Reads in a two column formatted RDC file where the first column contains the experimental RDC value and the second column contains the error in Hz for the value. In the case of only a single vector type, each line would correspond to the residue and missing data would be replaced with '999'. For more than one vector type, order for each vector needs to match the order specified by the user in the Prepare Input window.

Reads in a two column SPARKY format where the first column is the atom and bond label and the second column is the experimental RDC value. Currently only a single vector type at a time is supported for SPARKY.

Loads the RDC data column from another REDCAT file. If the currently loaded file is longer than the import RDC file, the extra equations, not present in the incoming REDCAT file, will be filled with 999's. If the currently loaded file is shorter, extra data in the incoming REDCAT file will be discarded.

Loads RDC data from a REDCRAFT formatted file.

### Save

- Save Redcat File
- Save State

Writes the current data loaded to a new REDCAT file.

Writes the current internal variables to a REDCAT State file

### Load

- Load Redcat File
- Load State

Loads a new REDCAT file. If there is currently a file loaded, it will need to be closed before a new file can be loaded.

Clears the currently loaded REDCAT file and resets all variables to default, then reads a new REDCAT State file and sets the internal variables accordingly.

### Close

Erases the data currently loaded so that new data may be loaded.

### Exit

Closes and Exits the program.

## Edit

### Select

Opens the Selection window which allows the user to select and omit equations loaded into the interface. Equations that are omitted will not be used in subsequent analysis and computations. For more information see the Selection section of the Main Gui page of this website.

### Options

Opens the Options window which allows the user to specify Error Padding, Set Error associated with each equation to a specified value, and/or change the location of the 2D and 3D SF map location. For more information see the Option section of the Main Gui page of this website.

## Tools

### Solution

#### Get Solutions

#### Generate Report

#### Ensemble Solutions

Displays the least squares solution (Tensor 0) as well as any Monte Carlo solutions generated. If the "Run" button has not been hit at least once since data was loaded into REDCAT, it will perform the Run operation and then display solutions.

Opens the Full Report window. After giving the maximum error value and clicking the "OK" button the following information is displayed: the Saupe Order Tensor Matrix; least squares solution; Da for the four common RDC types; R; 2D and 3D SF plots; error plot; and list of omitted vectors. For more information see the Full Report section of the Main Gui page of this website.

This opens the Ensemble Solutions window. Given an Ensemble REDCAT file and the maximum allowed error, this window allows analysis to be performed on multiple REDCAT files so that a side by side comparison can be made. For more information see the Ensemble Solutions section of the Main Gui page of this website.

### Error Analysis

#### Perform Error Analysis

#### Get Estimated Errors for All

#### Get Estimated Errors for Violations

Redisplays the output generated by clicking the "Run" button on the Main window. For each line, the equation number, the number of rejections, and the error value is shown.

For all equations, this command replaces the error value for the equation with the error calculated for that equation during the last Run.

For equations found to be beyond their specified error, this command replaces the error value for the equation with the error calculated for that equation during the last Run.

### Plot

#### 2D SF Plot

#### 3D SF Plot

#### Plot Vectors

#### Plot Violations

Opens the 2D SF Plot window. The least squares order tensor, as well as all other Monte Carlo solutions, can be plotted here. Plots can be manipulated with gnuplot commands directly, the data can be saved to a text file, and an image can be saved of the plot. For more information see the 2D/3D SF Plot section of the Main Gui page of this website.

Opens the 3D SF Plot window. The least squares order tensor, as well as all other Monte Carlo solutions, can be plotted here. Plots can be manipulated with gnuplot commands directly, the data can be saved to a text file, and an image can be saved of the plot. For more information see the 2D/3D SF Plot section of the Main Gui page of this website.

This opens the Plot Vectors window, which plots the RDC vectors on an 3 dimensional axis. This shows the directon and magnitude of the vectors. For more information see the Plot Vectors section of the Main Gui page of this website.

Plots violations for each equation. The x-axis is the equation number and the y-axis is the error in Hz. For more information see the Plot Violations section of the Main Gui page of this website.

### Rotate

#### Rotate PDB

#### Rotate Coordinates

Opens the Rotate PDB window. This rotates a PDB file using the Euler rotation scheme. For more information see the Rotate PDB of the Main Gui page of this website.

Opens the Rotate Coordinates window. This allows the currently loaded data to be rotated either by the Euler rotation scheme or, by an axis specified by line formed by three coordinates an a given angle to rotate about the specified axis. For more information see the Rotate Coordinates section of the Main Gui page of this website.

### Calculations

#### Calculate/Substitute RDC

#### Dynamic Averaging

Opens the RDC window. This window allows the back-calculation of RDCs from a provided order tensor and Euler rotation. The order tensor and rotation can be entered manually or selected the solutions provided by REDCAT. Random noise can be added, back-calculated RDCs may be substituted for selected equations, and a correlation plot may be created. The back-calculated RDCs are displayed, along with, RMSD, Q-Factor, and S-Factor. For more information see the RDC section of the Main Gui page of this website.

Opens the Dynamic Averaging window. This window allows the averaging of a selected domain over several different conformational states. For more information see the Dynamic Averaging section of the Main Gui page of this website.

## Help

### Help

This launches a browser window, or opens a new tab in a currently open browser, to the REDCAT Documentation pages found at http://ifestos.cse.sc.edu/REDCAT/documentation/.

### About REDCAT

This opens a dialog box with information regarding the Current version of the REDCAT GUI, information about principal investigator of REDCAT, and the current version of the REDCAT Engine.

### Contact Us

This opens the user's email thick client. An email may then be sent to valafarlab@gmail.com.

### Bug Report

This launches a browser window, or opens a new tab in a currently open browser, to the Contact Us page of this website.