Overview

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Copyright (C) 1999 - No portion of this program may be incorporated into other programs or sold for profit without express written consent of the authors.

1. Start the program by typing 'gsc'.

   If you do not get a graphical window, check with your system administrator to make sure the program has been installed and is accessible to you. If you customize the colors, fonts, size, etc of the window, these changes will be saved in your $HOME/.gsc file.

2. Enter the properly formatted shift file that you wish to study in the "Shift Data File" field and press return.

   Once the shift data file is entered, gsc will take a few seconds to read the shifts. It will display the sequence IDs of the first and last shifts read in the "xMin" and "xMax" fields respectively.

3. Next enter shift files for comparison in the "Compare File 1" or "Compare File 2" fields.

   The user can compare the shifts in the above data file to one or two other sets of shift data.

4. (optional) Change the "xMin" or "xMax" fields.

   This option is useful if you want to compare amino acids in a specific range of your sequence. Remember to press return after changing a number.

5. Select the atom you wish to study from the "Atoms" menu.

   Click and hold the mouse down and move the cursor to hilite the atom of choice.

6. Click the calculate button.

   The program calculates the shift differences. Understanding and saving the output is dealt with in the next two sections.

1. A line chart is drawn for each comparison file entered. The first line chart is represented by rectangles and the second by ovals.

2. Each rectangle/oval represents a matched amino acid shift difference. A match only occurs when:
   • amino acid ID numbers correspond (see renum_ppm)
   • amino acids are identical (eg, no substitutions)
   • both shift values are available

   A line connecting any two ovals or rectangles represents consecutively numbered amino acid ID numbers.

3. If an amino acid has more than one matching atom, then the averaged difference is plotted. An example of this would be glycine where HA1 and HA2 atoms can be matched between shift files.

4. At the bottom of the graph(s) the program prints the average error and correlation coefficient of all matched shift differences.

5. The "yMax" field determines the maximum and minimum numeric labelling on the y-axis. If "yMax" is set to 0, then the program will calculate a suitable value based on the shift differences it finds. A "yMax" greater than 0 means the program will not change the scale on the y-axis and will plot the points according to the current scale. Whenever the user changes the "yMax" field, the program will update the graph.

• Plot Width - the width of the plot area in pixels
• Plot Height - the height of the plot area in pixels
• Plot Background Color
• Title Text - A user defined title for graph(s)
• Title Color
• X-Label - text is written to bottom right corner of chart
• Y-Label - text is written to to left corner of chart
• X-Tics Start - amino acid to start labeling from
• X-Tics Increment - label each "nth" amino acid
• Y-Tics Num - number of labeled tics on y-axis
• Axis Color - includes x and y labels as well
• X-Axis Location - (middle, bottom, top, or none)
• Output Curve 1 - Color - color of line chart 1
• Output Curve 1 - Shape - select shape (either oval or rectangle)
• Output Curve 1 - Size - radius size of oval or rectangle in pixels
• Output Curve 2 - Color
• Output Curve 2 - Size
• Output Curve 2 - Shape

If you are looking to change colors of certain fields, a list of valid color names can be found in $OPENWINHOME/lib/rgb.txt or try /usr/X11R6/lib/X11/rgb.txt. Ask your system administrator.

The program has put the graph text in default areas. You can move any text by holding down the leftmost mouse button over the text and drag it to the area you wish. This may be useful when the text and graph lines overlap.

Fonts for the graph can be changed via the fonts GRAPHICS menu item. When selecting a font, it is desirable to select a postscript font available on your laser printer. Use the Save plot FILE menu option to save your plot to a postscript file.

It can be very insightful to look at specific atom shift differences for amino acids in greater detail.

The numeric shift differences that gsc has plotted can be viewed via the "show output..." FILE menu option. The user can also choose to save copies of the output files by selecting the "Save output..." FILE menu option.

The shift differences are printed one per line, and if more than 1 atom match is found in a given amino acid, then the average difference for that amino acid is also printed.

We felt that having more than two compare files would make it hard to read the graph. If the user really wants to depict several shift file comparisons on the same graph, you may be able to input the numeric output files into some other graph fitting package.

1. There can be data and non-data lines. Non-data lines are preceded with a comment character '!' in the first column.

2. Each data line contains one atomic chemical shift name and one or more shift value fields separated by one or more blank characters.

3. The atomic chemical shift name field is the first field and of the form:

   	molNum:Residue_ResId:atom
   

   where

   	molNum = Molecular Number (an integer)
   	Residue = Amino acid in 3 letter code (character string)
   	ResId = Amino acid ID number (an integer)
   	atom = Atom name (character string)
   

The shift name field has no blank characters and amino acids are expected to have ResId's which are ordered from lowest to highest. A shift value field is specified as a either a real number or with asterisks '*' to denote unknown values. The value "-999.99" or "999.99" is also understood by several programs to mean an unknown value.

Here is an example of a typical PPM shift file:

!
!Sequence: ADQ
!
1:ALA_1:N           ***.**
1:ALA_1:C           174.00
1:ALA_1:CA           51.90
1:ALA_1:CB           18.80 
1:ALA_1:HN          ***.**
1:ALA_1:HA            4.15
1:ALA_1:HB#           1.57
1:ASP_2:N           120.50
1:ASP_2:C           175.80
1:ASP_2:CA           54.70
1:ASP_2:CB           41.20 
1:ASP_2:HN          ***.**
1:ASP_2:HA            4.67
1:ASP_2:HB1           2.72
1:ASP_2:HB2           2.60
1:ASP_2:CG           **.**
1:ASP_2:HD2           *.**
1:GLN_3:N           119.60
1:GLN_3:C           175.80
1:GLN_3:CA           55.70
1:GLN_3:CB           30.20 
1:GLN_3:HN            8.24
1:GLN_3:HA            4.42
1:GLN_3:HB1           2.12
1:GLN_3:HB2           2.00
1:GLN_3:CG           33.70 
1:GLN_3:HG1           2.38
1:GLN_3:HG2           2.38
1:GLN_3:CD          180.00 
1:GLN_3:NE2         ***.**
1:GLN_3:HE21          7.37
1:GLN_3:HE22          6.71