GRAMMP (GRaphical AMMP)


   
GRAMMP is an extension of the AMMP program.  This new program has two windows: a command-driven AMMP window and a graphic's window.  

Features:



Click on the menu bar below to skip to menu descriptions

Portrait of GRAMMP


Manipulating the Molecule

There are several options for manipulating the molecule: rotation, scaling, slabing; using either the scrollbars or the mouse . The manipulation mode is set with the checkbox found on the Controls menu. For example, with the default setting of "Rotate (Y-X)", the horizontal scrollbar will rotate the molecule around the 'Y' axis while the vertical scrollbar will rotate the molecule around the 'X' axis. In addition, the mouse may be used to manipulate the molecule by clicking down the left mouse button while simultaneously moving the mouse. The molecule will rotate in the direction the mouse was moved.


Calculating Geometric Properties

GRAMMP provides various options for measuring the geometric properties of the molecule. The atom name, the distance between two atoms, the angle between three atoms, and the dihedral defined by four atoms all can be calculated. The user defines the current picking mode using the checkbox found on the Geometry menu. By clicking on a desired atom, the name of the atom will appear on a label next to the atom. Once the picking mode has been selected, the user must pick the appropriate number of atoms (2 for distances, 3 for angles, and 4 for dihedrals) by clicking on them. The user can simultaneously monitor distances, angles, and/or dihedrals.

 

Menu Explanations

File Menu

  Load AMMP file Dialog for to input an ammp file
  Output AMMP file Dialog for to output an ammp file
  Close Window Terminate the graphic's display
 

  Exit Terminate the graphic's display and quit ammp


View Menu

  Axis View down the X, Y, or Z axis
  Colors Change molecular colors: Monochrome (all white), CPK (CPK atom coloring),
Force (relative force coloring)


Controls Menu - manipulate the model

Rotate (Y-X) HSB*: Rotate around Y axis, VSB*: Rotate around X axis
Rotate (Y-Z) HSB*: Rotate around Y axis, VSB*: Rotate around Z axis
Translate HSB*: Translate left/right on screen, VSB*: Translate up/down on screen
Scale-Slab HSB*: Scale molecule, VSB*: Slab (i.e. clip) molecule
 

  Center on Last Atom Make the last atom picked the center of rotation
  Center on COM Make the center-of-mass the center of rotation
  Select Atom for Center Open a dialog box to select a specific atom as the center of rotation
 

Autocenter Continuously center the molecule within the graphics window
Autoscale Continuously scale the molecule within the graphics window
* HSB: horizontal scrollbar, VSB: vertical scrollbar


Geometry Menu - Calculate geometrical properties of the model

Atom Display an atom label for the next picked atom
Distance Display the distance (in Angstroms) between the next two picked atoms
Angle Calculate the angle (in degrees) between the next three picked atoms
Dihedral Calculate the dihedral (in degrees) defined by the next four atoms
 

  Clear Labels Remove all labels
 

Show Tethers Show atom tethers using a purple line
Show NOELS Show NOEL terms (atomic distance constraints) using red for unsatisifed constraint and green for satisfied
Show Violations Show only unstatisfied NOEL constraints


Ammp Menu - Execute AMMP Commands

  Dynamics Dialog for temperature constrained molecular dynamics
  Minimize Dialog for conjugate gradient minimization
  Torsion Search Dialog to define a torsion search
 

  Analyze Dialog for analyzing a range of atoms (e.g. the interactions of a ligand)
  Monitor Output energies for the entire molecule


Help Menu -

  On-line Launch Web browser to view these help pages




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Written by David S. Cavanaugh (4/99)