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
Here is an example CMap Image generated by the editor:
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:
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
and Wishart histograms, and (6) which information rows should be
Buttons and Options:
Selecting the colors for the CMap Image is done in 2 steps:
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)
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.
- Comments are specified by "#" and continue till the end of the line.
- A line starting with "Assignment_Info" must be present and immediately followed by a line with a list of Row Names (i.e. resonance rows, NOESY rows, etc.). There must NOT be extra lines between the "Assignment_Info" line and the Row Names line. This is then followed by a set of Residue Information Lines which may have blank lines. Together these three parts are called an Assignment Section.
- Multiple Assignment Sections are allowed with each starting with an "Assignment_Info" line, followed by the Row Name Line, and then by the Residue Information Lines. All the residues must be in numerical order in the first Assignment Section. Subsequent Assignment Sections may be sparse and out of order.
- The Row Name Line must start with "AA" or "Name" to represent the residue name. Subsequent Row Names may follow for Resonance, NOESY, J Coupling, Secondary Structure, Graphics, BarGraph Rows, or Spacer Rows.
- The Residue Information Lines start with the amino acid name followed by a value for each Row Name.
- Lines starting with "Settings:" are used to specify image settings.
- All values must be filled in. A "-" (minus sign) must be used to represent missing values.
- Phase information is represented by "P" after the number and is displayed as white vertical lines.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.
- NOESY Connectivity Rows start with "d" followed by a name which ends in include "(i+1)", "(i+2)", "(i+3)" or "(i+4)". NOESY values are represented using "+", where "+" means weak, "++" means medium, and "+++" means strong.
- Resonance Rows start with "C", "H", "N", or "M". The standard Resonance rows are HN, N15, CO, CA, CB, and HA. The name of the sequential part of a resonance row must include "-1". Other Resonance may be included. Resonance Rows starting with M are followed by a name. This name may have spaces by using a "_" character. This name may also have superscripts and subscripts by placing the selected text between "^" and "." respectively.
- Secondary Structure Rows start with an "S" followed by a name. The name may have spaces by using a "_" character. The name may also have superscripts and subscripts by placing the selected text between "^" and "." respectively. The Secondary Structure Row values are "h" for helix, "s"/"e" for sheet/extended, "t" for turn, and "-" for coil.
- J Coupling Rows start with a "J" followed by "2" or "3" representing the number of bonds and then the name of the J Coupling Row. The J Coupling values are "h" for helix, "s" for sheet, "hi" for helix indeterminate, "si" for sheet indeterminate, and "i" for indeterminate.
- Graphics Rows start with a "G" followed by a name. The name may have spaces by using a "_" character. The name may also have superscripts and subscripts by placing the selected text between "^" and "." respectively. You can also set the color of the row by using an "@" character followed by "A","B","C","D", or "T" to indicate the Graphics A, Graphics B, Graphics C, Graphics D, and Text colors. The Graphic Row values may be one to four "+" characters or numbers from 1 to 14. The different values give different graphic symbols. Also the color for an individual residue may be specified by using "A","B","C","D", or "T" as the first character of a Graphic Row value.
- BarGraph Rows start with a "B" followed by a name. The name may have spaces by using a "_" character. The name may also have superscripts and subscripts by placing the selected text between "^" and "." respectively. You can add line breaks using a "$" character. You can also set the fill and outline colors of the row by using an "@" character followed by 2 characters of "A","B","C","D", "T", "F", and "O" to indicate the Graphics A, Graphics B, Graphics C, Graphics D, Text, BarGraphFill, and BarGraphOutline colors. Two characters must follow the "@" character when indicating color choices. You can select the type of BarGraph by using a "?" character followed by "P" for positive bar graph, "N" for negative bar graph, and "B" for both. BarGraph Row values are floating point or integer numbers or "-". Also the color for an individual residue may be specified by using "A","B","C","D", "T" or "F" as the first character of a BarGraph Row value.
- Spacer Rows start with a "Z" followed by a name. The name is irrelevant, but numbers are probably best. The Spacer Row values are irrelevant, however, it is best to use a "-". It is probably best to have another Assignment Section for Spacer Rows and only have a single Residue Information Line with "-" values only.
- Reserved Rows Names: Do not use Row names that start with "P". This is use internally by the editor to represent the automatically generated Wishart Rows in the form of "PCA$CSI?B", etc.
Format: "Settings: Range RowName MinValue MaxValue"
# 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
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 - ++
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.
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