Using BTCL and TCL Commands To Manipulate the Geometry of Two Helices, Instructions

Copy the files helix.inp, helix.car, and helix.mdf from the directory $BIOSYM/tutorial/discover/ to a directory in which you have write permission
Read the example command input file to understand it--the commands are associated with comment lines (starting with #) and contain hypertext links to complete command descriptions.
A few hints to understanding the script are:
- Locate the beginning of the main commands section by finding the begin command.
- Understand the logic of the program by reading the comment lines first.
- Find the procedures fixorientation and writeheading and see how they are defined.
- Identify the TCL and BTCL commands useful for the following purposes.
  (Links are provided to one example of each--there may be other examples in the input file.)
  - Assigning values to variables.
  - Choosing a subset of atoms and the atom specification syntax. (The most general syntax is "molecule_name:residue_name:atom_name".)
  - Writing and calling a procedure.
  - Writing a for loop.
  - Using an if statement.
  - Opening a file and writing data to a file.
  - Using various molGeom and geometry statements to do geometry manipulation.
  - Using various vector statements to do vector and scalar operations.
Run discover 95.0 by entering at the UNIX prompt (indicated as %):
```
%   discovery helix
```
List the files in your working directory by entering:
```
%   ls -lt
```
Output files of the run should include helix.out, helix.cor, helix.arc, and helix.tbl
Examine the helix.out file (for example, with the UNIX more command). This is the default output name for the file that contains all the input lines in addition to the relevant output information.
Search for these output lines (links are included to the hypertext version of the helix.out file):
```
axis1 = line {{11.0926 17.2649 3.27548}} {{-0.821539 0.123481 0.55662}}
axis2 = line {{5.90624 11.5912 -3.12062}} {{-0.821539 0.123481 0.55662}}
line distance = point 10.0
point distance = point 10.0
```
The lines for axis1 and axis2 show the centroid, (the first { } in each line) and the direction vector (the second { } in each line) of the axes. Note that axis1 and axis2 have the same direction, indicating that they are parallel after execution of the fixorientation procedure. The line distance is the distance between two lines, and the point distance is the distance between two centroids. These two distances are the same, indicating that the centroids are lined up perpendicular to both axes at the predefined distance apart.
The helix.cor file is the coordinate file written out after fixing the orientation. It should contain two helices parallel to each other and 10.0 Å apart.
You can display the structures in the helix.cor file with the Insight program. Start up the Insight program from the directory in which you ran the Discover program by entering insightII at the UNIX prompt. Read in the helix.cor file with the File/Import command, and use Geometrics/Vector command of the DeCipher module to create the axes of the two helices by finding the least-squares fit line of the backbone atoms subset specified by molecule_name:*:ca,n,c.
(Before doing this, you might also want to display the molecules in the helix.car file to show that the helices in the original file were randomly oriented.)
Then use the Configurations pulldown of the DeCipher module to display all configurations (i.e., the ``trajectory'') of the different orientations of the two helices: the Configurations/Get command (to get the trajectory for the assembly called HELIX) and Configuratons/Animate command. The trajectory file is in the helix.arc file.
Use the Spreadsheet functionality to read in the helix.tbl file and then sort the energies in ascending order.

Do this by selecting the Spreadsheet icon, then selecting the Open command from the list that appears. Set the following parameter values:
File Type - Graph
File Name - helix.tbl
Object Name - Sheet
Select Execute.

Grab a corner of the spreadsheet window with the cursor and enlarge it to have a clearer view.
Use the Data/Sort command to sort the data, by setting the following parameters:

Extent Choice - Column
Primary Key - E0 (type it in or select the Total energy column by clicking the ``E'' column label)
Secondary Key - None
Tertiary Key - None
Descending Order - Off
Select Execute.
Now you can animate the configurations that have the lowest energies. First, you need to load only those conformations, with the Get/Configurations command. Enter the desired frame numbers in the Frame Spec parameter box, separated by commas.
Now you may be ready to try writing your own script to reorient a three-helix system or a four-helix bundle!

The annotated example input file (html, not ascii).
The example output file (html, not ascii).

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Helix Lesson, Introduction