QUANTA PRIMER

***this document gives instructions pertaining to the use of Quanta
   for molecular modelling of files imported from the pdb***

GETTING STARTED:

Before you begin your work with Quanta, you should import the file you plan 
to work with from the Brookhaven Protien Data Bank into the directory in which
you plan to use Quanta. To start quanta enter the following commands:

	athena%add molsim
	athena%source /mit/molsim/quanta4.1.1/quanta4.1/.setquanta
	athena%quanta

A message may appear stating that your directory does not contain the necessary
startup files and asking whether default files should be used. Click on YES.
At this point the Molecule Window should appear on you screen. (Warning:
Sending zephyrgrams while the molecule window is open may cause you to
lose your work.)To open the file you have imported from the PDB, choose 
IMPORT from the FILE menu. Then highlight the file you wish to import
and click on IMPORT. The file you have selected should now be displayed
in the Molecule Window.

MOVING AROUND THE MOLECULE:

A.USING THE DIAL EMULATORS:
	1)CHANGING THE VIEWING ANGLE: To rotate the molecule, move the 
		cursor to the Dial Emulator Window. Place the cursor on
		one end of the Z ROTATE button and click the left button
		of the mouse several times. Try holding down the mouse 
		button. Next, move the cursor to the other end of the
		Z ROTATE button and hold down the mouse button to rotate
		the molecule in the other direction.Using the X-, Y-,
		and Z ROTATE buttons, turn the molecule until any bonds
		of interest are clearly visible.
	2)CHANGING THE POSITION OF THE MOLECULE: The molecule can be 
		moved around the screen using the X- and Y TRANSLATE 
		buttons. The Z TRANSLATE button can be used to move
		the molecule closer way from the viewer.As the molecule
		is moved into the screen, the segments at the back of
		the molecule will start to fade and disappear. As
		the molecule is moved forward the front ofthe molecule will
		gradually disappear, as if the viewer is moving through
		the molecule.Moving the morward, then, is one way to
		observe important sites that may be buried within the
		center of the molecule.
	3)VIEWING CROSS-SECTIONS OF THE MOLECULE: Position the cursor
		slightly to one side of the center of the CLIP button.
		Holding the mouse button down, move the cursor slowly
		outwards to narrow the width of the viewing section.
		Next, move the cursor to the Z TRANSLATE button and move 
		the molecule forwards and backwards to observe different
		cross-sections.
	4)CHANGING THE SIZE OF THE MOLECULE: The molecule can be marger or 
		smaller by holding the mouse button down as you slide the
		cursor left or right from the center of the SCAL button.
	5)RETURNING TO THE ORIGINAL SETTINGS: The molecule can be returned
		to its original settings by clicking on the RESET button.

USING PALETTES

	1)MOVING AROUND A FRAGMENT: Selected fragments of a molecule can
		be rotated and translated by selecting the MOVE FRAGMENT
		options from the MODELING palette. Then choose the desired
		fragment by clicking on the atom you wish to designate as
		the center of motion. After experimenting with several
		different conformations, return the fragment to its 
		original position by selecting UNDO CHANGES from the 
		MODELING palette. Then click on number 1 in the bottom
		of the DIAL EMULATOR window to revert to the default commands.
	2) MOVING AROUND AN ATOM: Selected atoms can be translated
		by choosing the MOVE ATOM command from the MODELING palette.

USING THE MOUSE:

As and alternative to the methods described above, the mouse can be used in 
conjunction with the keyboard to manipulate the displayed molecule. A list of
associated mouse/keyboard commands is included on the last page of this
primer. ***List is from Quanta BASIC OPERATIONS manual***

DISPLAYING STRUCTURES AND BONDS: 

When an entire protien molecule is displayed the screen can get quite
cluttered. In order to see many of the important characteristics of the 
protien it is often necessary to highlight or hide various structures and 
bonds.

	1)STRUCTURES: Click on DISPLAY ATOMS in the DRAW menu to open the
		DISPLAY ATOMS menu. Clicking on SELECTION TOOLS will open
		the DISPLAY UTILITIES and DISPLAY ATOMS palettes. Some of
		the following commands are particularly useful for 
		displaying and hiding important molecular structures.

		All Atoms  	  Displays all atoms in structure
		Non-H Atoms   	  Displays all but H atoms in structure
		Protien Backbone  Displays only protien backbone atoms
		C-Alpha trace	  Displays tracer line that connects the alpha
				   carbons in a protien
		Solvent		  Displays solvent molecules
		Residue Range	  Displays selected sequence of residues
				   (enter the #s of the first and last 
				   residues to include)
		Residue Types	  Displays selected residue types 
				   (i.e., Ala and Leu)
		Mark Selected
			 Atoms	  Marks selected atoms with an asterisk
		Include		  Includes all subsequently selected options
		Exclude		  Excludes all subsequently selected options
		Undo		  Undoes last selection
		Revert 		  Returns to original state
		Quit		  Exits without saving
		Finish		  Displays changes and exits palette
 
	2) HYDROGEN BONDS: Hydrogen bonding positions can be determined by
		 choosing HYDROGEN BONDS from the CALCULATE menu. Next choose
		 CALCULATE HBONDS. To hide the hydrogen bonds once they have
		 appeared click on SHOW HBONDS (which had been automatically
		 selected) to turn this selection off. ***Any time changes are
		 made to atoms or bonds in the structure, hydrogen bonds must
		 be recalculated.***

	3) RIBBON DIAGRAMS: Ribbon Diagrams are a useful way to demonstrate
		 secondary structure in the displayed molecule. To generated a
		 ribbon diagram, choose the CREATE OBJECTS option from the 
		 DRAW menu. Select RIBBON from the menu and click in the box 
		 next to ATTATCH TO MSF to choose this option if it is not
		 already highlighted, then exit by clicking on OK. The ribbon 
		 diagram will appear on the screen, along with an OBJECT
		 MANAGEMENT table. To turn off the ribbon diagram, move to the
		 OBJECT MANAGEMENT table and click over the word YES in 
		 the DISPLAY column to change it to NO. The ribbon diagram 
		 will disappear, but it will be attatched to the file for 
		 future use.
  
CALCULATING BONDS AND DISTANCES:

	1) DISTANCES: The sizes of molecules or structures within molecules 
		 can be determined by measuring the distances between selected
		 atoms. First, make sure that SHOW DISTANCE MONITORS is
		 selected from the GEOMETRY palette. Next, select the DISTANCE
		 option. Select one of the atoms by positioning the cursor
		 over the atom and clicking the mouse button. Select the
		 second endpoint atom in the same manner. The distance between
		 the two chosen atoms will then be displayed in the textport
		 window. Another option, CONTINUOUS PICK MODE can be used 
		 together with DISTANCE to measure the distances between each
		 set of neighboring atoms in a series of selected atoms.
		 Reselect either option to turn the function off.

	2) DIHEDRAL ANGLES: Dihedral angles occur both in the protien
		 backbone, where they are known as phi-psi anglse, and in
		 amino acid side chains, where they are refered to as side
		 chain torsion angles. These angles can be measured using the
		 DIHEDRAL option from the GEOMETRY palette. The SHOW DIHEDRAL
		 MONITORS should be selected, while the two other MONITORS
		 options should be off. Clicking on the four atoms that define
		 the dihedral angle in succession (as shown below) will then
		 produce an angle measurement in both the Textport Window and
		 in the viewing area.

COLOR SELECTION:

	1) CHANGING THE DEFAULT COLORS: The default colors can be changed by
		 clicking on 5 or 6 at the bottom of the Dial Emulator Window.
		 Holding the left mouse button down while the cursor is
		 positioned over the H, S, or I button will slowly change the
		 hue, saturation, or intensity respectively. Changing the
		 default colors can be especially useful when structures of
		 interest are colored similarly. To return to the default
		 coloring choose COLOR DEFINITIONS from the PREFERENCES
		 menu, followed by RESET ALL.

	2) COLOR BY STRUCTURE: From the DRAW menu, choose COLOR ATOMS and pull
		 right to open the menu. Choose to color by element, segment,
		 or molecule, or pick SELECTION TOOLS to open the COLOR ATOMS
		 and COLOR SCHEMES AND UTILITIES palettes. The chosen 
		 structures will be colored according to preset guidelines.
		 For example, choosing PROTIEN SIDECHAINS from COLOR ATOMS
		 and AMINO ACID BY POLARITY from COLOR SCHEMES AND UTILITIES
		 will result in different coloring for basic, acidic, and 
		 nonpolar sidechains. (Simultaneously labelling by residue
		 name will show which color corresponds to which of these
		categories.

EXITING QUANTA:

When you are done working with Quanta, be sure to save any changes you have
made to the molecules you are working with by selecting SAVE CHANGES from
the MODELING palette. Choose CREATE A NEW GENERATION and click on OK. Next go 
to the file menu and select CLOSE. Choose CLOSE ALL, then click on OK.
Finally, choose EXIT QUANTA from the FILE menu.