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

Click here to go immediately to the tutorial lesson itself.

• Specifying atoms (more examples can be found in the documenation of the select command).
• Creating a subset of atoms for a system, e.g., backbone atoms, using the subset command.
• Finding the axis of a helix by finding the least-squares fit line for the backbone atoms, using the molGeom get lsqLine command.
• Rigidly rotating a molecule around an axis, using the molGeom rotate command.
• Translating a molecule using the molGeom translate command.
• Calculating the energy using the energy command.
• Using the geometry command to find:
  • The angle between two line using geometry ang1 angle line1 line2
  • A point on a line using geometry point1 point line1
  • The direction vector of a line using geometry vec vector line1
  • The distance between a point and a line using geometry dist distance point1 line2
  • The distance between two lines using geometry dist distance line1 line2
• Using the vector command to find:
  • The cross product between two vectors using vector vec3 cross vector1 vector2
  • The negation of a scalar or vector using vector argout negate argin
  • The difference (subtraction) between two scalars or vectors using vector output subtract inarg1 inarg2
  • How to change an angle from radians to degrees using vector angdegree degree angradian (This is necessary because the geometry command works in radians but the molGeom command works in degrees)
• Printing data to a file using the writeFile command.
• Setting a variable using the set command.
• Writing a for loop to do repeated operations.
• Opening a file by using the open command.
• Writing a procedure using the proc statement.
• Writing a conditional if statement.
• Writing out data using the puts and echo commands.
• Using format statements to print in formatted form.
• Using the Insight spreadsheet to sort the energies in ascending order.
• Using the Analysis/Trajectory command of the Insight interface to replay various orientations of the helices and their energies.

Some Basic Concepts concerning TCL and BTCL

This is a very flexible language allowing you to write procedures (or subroutines), control the flow of the program using conditional statements (e.g., if) and do repeated operations (e.g., for). It allows you to write customized application procedures at the user-interface level instead of having to modify the program itself.

A few basic concepts are central to understanding BTCL:

1. ALL TCL argument variables are strings, and the symbol $ is used for variable substitution or returning the value of a variable.

   For example, in the MAIN COMMANDS section of the input file example that accompanies this tutorial:

      $mindist = 10.0
   

   This assigns the value of the variable mindist to be 10.0. When this value is later passed to the procedure fixorientation, $mindist has to be used instead of only mindist. Using the latter would cause an error, because the program expects a number, but mindist is a string.

   Another example in the MAIN COMMANDS section is:

      for {$j = 0} {$j <= $numspin} {incr j} {
   

   works, but

      for {$j=0} ....
   

   does not.

   This is because TCL interprets $j=0 as one string variable and there is no such thing. Hence it is important to put a space between a variable and an operation sign.

2. All commands have the same syntax. It is:

   Command argument argument ...

   For example, in the definition of the procedure in the input file called fixorientation:

       geometry ang12 angle $axis1 $axis2
   

   geometry is the command, and ang12 angle $axis1 $axis2 are all arguments.

   However, not all arguments have the same function. Here, ang12 is the output and is the angle between the input lines $axis1 and $axis2. The argument angle is the operation that performs one of the functions that the geometry command is capable of performing. While ang12, axis1, axis2 are variables you can choose, angle is the operation and is defined by Biosym/MSI.

   The reason why ang12 does not have a $ is that the value of this string variable has already been updated in the subroutines that perform the geometry command.

3. BTCL includes ``geometry objects''. The content of these objects, for example, $axis1, gives you only the reference point to get the values of these objects.

   For example, use:

       echo $axis1
   
       geometry#5
   

   To print out the value of that geometry object, the geometry command has to be used:

       echo axis1 = [geometry $axis1]
   
       axis1 = line {{11.0926 17.2649 3.27548}} {{-0.821539 0.123481 0.55662}}
   

   where the first { } contain the x, y,and z coordinates of the centroid of that line and the second { } contain the direction of the line.

4. Commands are terminated by a semicolon (;) or the end of the line. In loops and procedures, an open brace { can serve as the end of the line also.

   The backslash \ at the end of a line indicates that the following line is a continuation of that line. Make sure there is no space after the backslash.

5. Procedures have to come before the main commands section, which starts with the begin command.

6. BTCL is case sensitive. For example, molGeom works but molgeom does not.

Helix Lesson, Instructions

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

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