CalcMol Beta2 83 Readme
======================

CalcMol is program that is completely unconnected to RasMol that displays molecules on your calculator. Now it is also available on the TI-83!!!

The file format is simple (once you understand it). List 'x' stores the X coordinates, list 'y' stores the Y coordinates, and you can guess what list 'z' stores. List 'BX' stores the bond configuration.

Here are sample 'x', 'y', 'z', and 'BX' lists:

x    |y    |z    |BX   |
-----+-----+-----+-----+
1.000|1.000|0.000|1    |
1.000|0.000|1.000|2    |
0.000|1.000|1.000|1    |
     |     |     |3    |

Each odd-numbered element in list 'BX' (the 1's in the example) are start "atom". CalcMol goes to these "start atoms" (in this case, only "1" is a start atom, so all bonds originate from atom number 1.) in the 'x', 'y', and 'z' lists and draws a bond to the neighboring element (in this case, 2 and 3). What you are telling CalcMol to do is draw a bond from atom 1 to atom 2, then another bond from atom 1 to atom 3. Obviously, lists x, y, and z need to be the same length or your TI-83 will return an error.

All of the coordinates are in angstroms (supposedly), but usually it doesn't matter as long as all the bond lengths are appropriate lengths.

As you may have noticed, coordinates for atoms can be obtained from Brookhaven Protein Databank files. Bonds, however, usually have to be manually entered because the "automated" process is too hard too explain and too risky.


!!!!Addendum!!!!
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When it asks you for the number of atoms, you can just type 'AUTO' (all caps) if you don't know how many atoms there are. This function is so that people can only draw portions of a molecule or a substrate from a substrate-catalyst combination.


To-Do
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- Speed up the program, though it isn't too slow even under Emu8x.
- Fix new file version support--the TI-83 Plus Beta2 has a new file version that is much faster.
-Suggestions, anyone?