Theoretical Aspects

Summary

How to use MODULE
 

Required Material

Starting the Program

Input File Format

Initial Display

Displaying the Primary Sequence

Selection of Type of Coupling

Setting Internuclear Distances

Fitting Single Modules

Fitting the Alignment Tensor

Correlation Plots

Comparision of Calculated and Experimental Couplings

Monte Carlo Error Analysis

Test Sample 1

Choice of Modules from Primary Sequence

Fitting the Alignment Tensors

Correlation Plots

Comparision of Calculated and Experimental Couplings

Monte Carlo Error Analysis

Common Alignment Frame

Degenerate Orientations

Automatic Calculation of Molecular Architecture

Covalent Bonds

Test Sample 2

Special Cases

Axially Symmetric Alignment Tensor.

Highly Rhombic Alignment Tensor.

 
Distance Constraints

Creating and Reading Work Folders

Simulating Datasets

Hammerhead Ribozyme - Orientation of Secondary Structural Motifs.

Test Sample 3

Protein-Protein Complexes.

Test Sample 4

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Required Material

Silicon Graphics running IRIX 6.5 or higher, PC Linux running RedHat 5.2 or higher, or SUN SPARC running Solaris 2.6 or higher.

Starting the Program

The program is started by typing the command module. Data and coordinate files can be read using either the name of the files -

or by reading the files in the File menu -:

Input File Format

Module requires two sources of input information: the measured residual dipolar coupling values D_ij, their associated uncertainty s_ij and an estimation of the order parameter S (for many application this will of course be assumed to be 1), and a standard coordinate file from the Brookhaven data bank containing the structure under investigation (protein or nucleic acid).
 

_{The data file must be of the form -}

3 CA 3 C     -2.127479 0.195 1.00

4 CA 4 C     1.182786 0.349 1.00

5 CA 5 C     3.222452 0.245 1.00

- - - - - - -

- - - - - - -

2 N 2 HN     10.013671 0.500 1.00

3 N 3 HN      6.264468 0.500 1.00

4 N 4 HN     15.149721 0.500 1.00

5 N 5 HN     -8.166057 0.500 1.00

- - - - - - -

- - - - - - -

These lines can be entered in any order. The program will recognise any atoms whose equivalent names are present in the pdb file, so no sub-headings are required.
 

Initial Display

The initial display of the program shows the molecular structure in the pdb reference frame:

Displaying the Primary Sequence
 
 

The molecular sequence can be displayed by selecting the option Definition from the Visualisation menu -
 
 

Selection of Type of Coupling
 

MODULE can treat different couplings simultaneously or in combination. To select the couplings to be treated for a given tensor calculation select Couplings Choice from the Control menu : The available couplings in the data file will be already highlighted and can be selectively removed by clicking on the illuminated box.
 
 

Setting Internuclear Distances
 

The couplings are calculated with the appropriate pre-factors including the gyromagnetic ratio and the inter-nuclear distance; this can be chosen to be a either a standard fixed distance from an interactive table, or the actual distance (Å) present in the coordinate file (select Inter-Atom Distances from the Control menu)
 
 

While the program has been specifically designed to treat multiple structures simultaneously, in the simplest case the whole molecule will be considered to be a single module, and a single tensor will be fitted - all amino acids for which data are available have a dot above the appropriate letter in the primary sequence.