SNC DDG Calculator
Latest build	0.2	2003.09.28

Introduction:
	SNC DDG Calculator is a patch data analysis tool developed for
Wavemetrics Igor Pro versions 4 and higher. The entire program is contained in a
single procedure file, which can be downloaded from http://igor.qiguang.net. The
main function of this program is to read in V_half and Slope values from 
Boltzman-fitted G-V curves and calculate DG and DDG values, average these values, 
and create graphs to represent the averaged DDG data. This program is still in 
active development, and new features/bug fixes are being addressed as they arise. 
If you use this program, you are encouraged to e-mail questions, comments and 
suggestions to igor@qiguang.net.

Known bugs:
	All known bugs from previous version (0.1b) have been fixed in the current 
version (0.2).  If you run into a bug, please send e-mail to igor@qiguang.net.
	
Notes on usage:
	If you downloaded the experiment file (.pxp), just open the file with Igor 
and you should be able to start using the program.  If you've downloaded the 
SNC_DDG_Calculator_v.0.2.ipf file, open Igor and load the procedure file.  (You do 
not need globals2.ipf or working2.ipf.)  

	The program needs V_h and Slope values.  You can supply these values by 
either typing the values directly into the program or typing the values into a text 
file and having the program load that file.  The first approach involves creating a 
new mutant (using the "New Mutant" button) and inputing V_h and Slope values into 
the input dialogues that are then displayed for you.  The second approach requires 
an understanding of the file structure that the program recognizes.
	
Notes on Patch Data File Structure:	
	This is probably the most useful feature of the program, since it makes
it very easy to modify a huge set of data and have the program create a whole
new set of graphs reflecting the change in the data with minimal additional effort
from the user.  The file should be a text file (.txt) and can be edited in
Notepad.exe or any other plain text editor.  Comment lines are indicated by a
"#" symbol at the beginning.  The first non-comment/non-empty line of the file
must contain the following line:
	
	filetype	SNCPatchData
	
Upper/lower and space/tab doesn't matter. Patch data are grouped by mutant, and
each group contains a mutant header line and a mutant termination line.  The
mutant header and mutant termination lines have the format:
	
	mtinfo	name=NAME	number=NUMBER	solutions=[SOLUTIONS_STRING]
	
	/mtinfo
	
NAME can be any text string (i.e. E324A).  NUMBER can be any number, and can
even include letters (i.e. 50, 50a). SOLUTIONS_STRING has the format:
	
	#:# [#:#...]

where the # symbols indicate numbers.  Each number pair (#:#) indicates Ca:Mg
ion concentrations.  The SOLUTIONS_STRING can contain any number of number
pairs, but this program has only been thoroughly tested with 4 number pairs (4
solutions).  The number pairs must be separated by either a blank space (" ") or
an underscore ("_").  An open ("[") and close ("]") bracket must surround the
SOLUTIONS_STRING.

	The patch data goes in between the mutant header and mutant termination
lines.  The order of the data must be all V_half values first, then Slope
values:
	
	V_half [V_half...] Slope [Slope...]
	
Each value must be separated from adjacent values by one or more space(s) and/or
tab(s).  The number of spaces or tabs does not matter.  If a value is missing,
"NaN" must be typed in place of the missing value.

Notes on Saving File:
	Remember to save your work after you're done!  The actual data that will
be saved is the patch data (V_half and Slope values, along with mtinfo lines).
The program automatically calculates DG and DDG values whenever you load a file,
so there's no need to save DG and DDG values.  Be careful of overwriting old
files.  If you want to be safe, you can use different files for each session.
If you're pretty sure about what you're doing, you can use the same file for
every session.  It's up to you.  When you click the "Save File" button, you will 
be presented with a dialogue box to chose the file you want to save to. Remember, 
you can always see what is in a patchdata file by opening it up in any text 
editor.
	
Notes on How Waves are Used and other Tidbits
	This is for those who are interested in editing the waves that contain 
patch data, Z values, and DDG values.  It is not necessary to know this 
information, but if you are curious in how the program works or want to edit 
previously entered raw patch data through Igor's wave tables, then you should 
read this section.

	When either a file is read or a new mutant is created in the program, 
a wave called "PD_%" is created where % is replaced by the name of the mutant 
(i.e. E324A).  This wave stores Vh and Slope values and is two dimensional, with 
each row representing a unique patch.  Horizontal values are read as Vh first, 
then Slope.  The order of these values correspond to the solutions description 
defined by the user.  DDG and averaged DDG values are stored in "DD_%" and "ADD_%" 
respictively.  Z and averaged Z values are stored in "Z_%" and "AZ_%." Averaged Vh 
values are stored in "AV_%," and averaged Slope values are stored in "AS_%." The % 
in these waves are mutant names, like above.  When graphing, the program creates a 
wave to store x-axis units called "catX_Units" and creates waves called "catY_%" 
which it graphs against "catX_Units."  The % in "catY_%" depends on what is 
currently being graphed, and is most likely taken from the dimlabel of either 
"ADD_%," "AZ_%," "AV_%", or "AS_%."

Notes on Graphing:
	The graphs are probably the most visually pleasing and informative
aspect of the program.  There are numerous options available.  They are all 
pretty self explanatory. If you have any questions, feel free to e-mail me. 

That's all for now.

Steve
stevec@qiguang.net
http://igor.qiguang.net