Connectivity Map Image Editor

Contents


Overview

A Connectivity Map Image represents resonance and other residue specific information in a graphical form.  The CMap Editor breaks each type of information into information rows (resonance rows, NOESY connectivity rows and Wishart Histograms) that the user can then manipulate graphically.  The information rows can be moved around, deleted, and have their appearance altered graphically in various ways. The editor can print the desired images or save them in GIF format. The editor starts with reading the information in a specific flat file format. 

Here is an example CMap Image generated by the editor:

CMap Image


Main Editor Window

A new CMap Editor Window to brought up when the user selects the "Connectivity Map Image" Tools menu option.  Below is a blank CMap Editor Window:


CMap Editor

Buttons:

  • Open File - read in an image input file and create the image.
  • Reread Data - rereads the image input file. If the user modified the input file, the changes will be visible in the image. Note: this button will reset the image to one set of rows.
  • Cut Image - if the cut lines have been created, cuts up the image into multiple sets of rows.
  • Start Over - after the image has been cut up into rows or after cut lines have been created, pressing this button resets the image back to one row and all the cut lines are removed. Note: this button will not update image if the values in the image input file have been changed.
  • Options - opens the Options window where the user can select the options for viewing the image.
  • Save Wishart - opens a dialog where the user can select the location of the output file to save calculated Wishart CSI information
  • Print Image - opens a print dialog where the user can select where to print this image - either to a printer or to a file (postcript).
  • Save Image - opens a save dialog where the user can specify where to save this image. Note: the image is saved as GIF.
  • Close - closes this window.
  • Help - opens an appropriate browser with the help page (brings up this page).

After "Open File" button is pressed, the user can select the image input file which is read in and the image is created. If the user modifies the image input file, the image can be updated by pressing "Reread Data" button.

When the mouse hovers over the image, a vertical line is drawn where the mouse is. This line represents a possible cut line. If the user clicks with the left mouse button on the image, a cut line is drawn. This cut line represents where the image will be cut. The user can either create all cut lines at once and then press "Cut Image" button, or the user can create one cut line, press "Cut Image" button, create another cut line, press "Cut Image" button, etc. Usually, it's easier to see the current version of an image if the cut lines are creates one a time. After the image is cut, an appropriate number of rows is created, depending on the number of cut lines. Each set of rows has the same information rows (resonance, NOESY and Wishart Histograms). Please note that the image can be cut only between residues.

If the user decides that they made a mistakes where the cut lines are placed, they can press "Start Over" button, which shows the image all in one row.

If the user wants to save an image to a file, they can press "Save Image" button and the image will be saved in the file specified by the user. Note that the image is saved as a GIF. Similarly, if the user wants to print an image to a printer or to a file (as postcript), they can press "Print Image" button. Please note that the quality of an image is better if it is saved first as a GIF and then printed from another program (netscape or photoshop, for example). Also, note that the cut lines will NOT be saved/printed in the final image.

If the user wants to change what is displayed in the image, they can do so in the Options Window by pressing "Options" button. Here is what can be modified: (1) lines beween residue, (2) arrows on NOESY lines, (3) relative scale of the image, (4) relative font size of the image, (5) color of intra/sequential links, NOESY lines and Wishart histograms, and (6) which information rows should be visible.


Options Window

Options Window

Buttons and Options:

  • Lines Between Residue - the user can select whether the lines between each residue are displayed over or under the links, or not displayed at all.
  • Show Arrows - the user can select whether the arrows for the NOESY lines should be drawn. If there is an arrow at the end of the NOESY line, this means that the line is too long for this row and this NOESY line is 'continued' on the next row. And on the next row, there is a corresponding arrow representing that this line is the continuation of a NOESY line from the previous row.
  • Relative Image Scale - the user can select the scale of the CMap Image - i.e. how large/small the image is. Only integers are allowed as scale numbers. Initial scale is 100%, and the scale can range from 50% to 1000%. As the scale is modified, the font size is modified accordingly.
  • Relative Font Size - the user can select the font size that is used in CMap Image to draw the residue names, dimension labels, etc. The font size starts out as '14' and can range from 5 to a very large number. As the scale of the image is modified, the font is modified accordingly. For example, if the scale is changed from 100% to 200%, and the original font size is 14, then the font becomes 28.
  • Change Colors - the user can select what colors to use for intra/sequential links, phase, weak/medium/strong NOESY lines, lines between residue, and Wishart histograms.
  • Change Row/Column Size - the user can modify the height and width of information rows. The sizes are specified in pixels.
  • Select Visible Information Rows - the user can select which information rows are visible in the CMap Image.
  • Change Row Order - the user can change the order in which the rows appear.


Color Options Window


Color Options Window

Selecting the colors for the CMap Image is done in 2 steps:

  • STEP 1: Select which color option to modify. For example, if the user wants the Weak NOESY lines to be blue, then they should select "NOESY - Weak" radio button. A rectangle is drawn around the selected color option.
  • STEP 2: Type in the desired color values (1-256). The user has the option of selecting two types of representation of color: "Color" and "B & W" (Black and White). If "Color" is selected, then the user can type in Red, Green and Blue values to represent many colors. If "B & W" is selected, the user can type in one Gray value to represent the shade of gray. As the values are typed in, the color sample next to the color option is modified to display the current color and the CMap Image is modified also to the new color. For example, if the user wants to modify the Weak NOESY lines to blue, "Color" option should be selected and the following values should be typed in: R: 1   G: 1   B:256.

Buttons:

  • Save Current - saves all the current colors
  • Recover from Save - recovers from the last set of colors that were saved using 'Save Current' button
  • Default B/W - sets all the colors to predefined grayscale colors.  This is the default color scheme.
  • Default Color - sets all the colors to predefined colors.
  • Default Inverse - sets all the colors to predefined colors with the Background and Text colors inverted.
  • Close - closes this dialog
  • Help - opens a browser (specified in the preferences) with the help page on how to use this dialog (opens this page).

Row/Column Size Options Window


Row Column Size Options Window

Sections:

  • Row Heights - the user can select the heights in pixels of each major type of Information Row.
  • Row Widths - the user can select the width in pixels to display each residue's worth of information.
  • Label Length - Length of the each Information Row's Label in characters.

Row Visibility Options Window


Row Visibility Options Window

Description:

This window allows a user to select which Information Rows are currently visible in the CMap Image. If the checkbox next to the name of the information row is checked, then this row is visible; if the checkbox is unchecked, then this row is not visible. The user can also (un)select a collection of rows based on the type of the row. The four categories of row are labeled at the top of the dialog: Resonance Rows , NOESY Rows , Wishart Rows ,  and Misc Rows. (Un) selecting the header choices, (un)selects all the rows below the header. Note that Resonance and NOESY rows are read in from the image input file, whereas, Wishart rows are predefined (and calculated) by the program. There are two general types of Wishart Histograms implemented in AutoAssign: CSI and Delta. CSI represents the chemical shift index determined by a formula (Wishart, 94). In the 'Consensus-CSI' histogram, the values are determined using the 'majority rules' algorithm (two out of three, or three out of four).  Each value in the Delta histogram is the difference between the chemical shift value observed and the random coil value from a table. In the 'Consensus Delta' histogram, the values are determined from the following formula:
(CA-Delta) - (CB-Delta) - 5 * (HA-Delta)


Row Order Options Window

Row Order Options Window

Description:

This window allows the user to select the order of Information Rows in the CMap Image.  Each Information Row can be selected by its corresponding radial button.  Then the Move Up and Move Down buttons can be used to move the selected row up and down in the row order.


CMap File Format

File Layout and Format:

Value Formats:

Some residues require two values. To specify that two values are expected, these values must be placed in a list between parenthesis. An example is: (5.02 6.03). If both values are present, the corresponding link in the image has a small 'bump' to show that the two expected values are present. If one value is missing when two values are expected, then the corresponding link in the image has a 'dent' or a 'hole' representing that one value is missing when two are expected. An example of one missing value that can be specified in the image input file is: (5.02 -). Another way to represent that one of the two values is missing is: (5.02). It is recomended to use "-" to represent missing values because it is easier for the user to look through the input file and see which values are missing. An example of both values missing is: (- -) or simply "-". Please note that the values between parenthesis do not have commas between them. Placing commas will generate an error.

Row Type Formats:

Settings Formats:

Format:   "Settings: Range RowName MinValue MaxValue"
Format: "Settings: RowOrder RowName RowName ... "

Example File:

# This is an example image input file (this data is modified from original for 
# example purposes)
# (1) this input file has two 'sets' of information rows
# (2) this file has information for 7 residues
# (3) Residue "L6" has Phase information for "CO-1" resonance row ("179.2P")
# (4) Residue "D3" is expecting to have two values for "HA-1" resonance row, but
# only has one value in the list -> since one value is missing, this will be
# represented as a 'hole' in the corresponding link in the image
# (5) Residue "G5" is expecting to have two values for "HA" resonance row and has
# both values -> since both values are present as expected, this will be
# represented as a 'bump' in the corresponding link in the image


Assignment_Info
AA HN N15 CO-1 CA-1 CB-1 HA-1 CA CB HA dAN(i+1) dAN(i+2)
R1 --- - - - - - - - - + +++
P2 - - - - - - - - - ++ +++
D3 - - - - - (5 -) - - - + ++
F4 7.81 116.5P 176.6 57.6 40.0 4.4 59.4 37.6 4.78 +++ -
G5 7.43 121.1 179.2P 59.5 37.6 4.76 58.1 39.9 (4.56 5.2) ++ +
L6 7.54 113.7 183.4 58.1P 39.8 4.55 55.0 41.8 4.67 + ++
E7 7.49 120.4 178.2 54.9 41.9 4.71 55.1 30.9 4.73 - ++


Assignment_Info
AA dAN(i+3) CE CE-1
R1 +++ - -
P2 +++ - -
D3 +++ - 129.5
F4 ++ 129.5 -
C5 + - 42.4
L6 - 42.4 -
E7 - - -


#
# Graphics Row starts with G and has its color set to Graphic A. Its C5 value will use Graphic C color.
#
# BarGraph Row has a superscript of "2". It has its fill color set to Graphic B and its outline color set to Text.
# It is set to a "positive" bar graph type.
#
# Secondary Structure Row has 4 residues marked as helix and two marked as turn.
#
Assignment_Info
AA GHN_Exchange@A BS^2^@BT?P SS
R1 - 0.75 -
P2 +++ 0.77 h
D3 +++ 0.81 h
F4 ++ 0.75 h
C5 C+ 0.68 h
L6 - 0.64 t
E7 - 0.54 t