A. Main Menus

Table 29. File menu functions and commands 

Selection	Pull-right selection	Generated commands	Description
Open		mole open	Opens MSF files list for selection.
Close		mole close	Closes current MSF.
Save As		msf create	Saves current MSF.
Revert		msf undo	Reverts to previous MSF.
Copy MSF		msf clone	Makes a copy of current MSF.
Import		data import	Brings external files into QUANTA.
Import Multiple PDBs		data pdbs	Imports more than one PDB file at a time.
Export		data export	Sends QUANTA files to external applications.
Sequences ->	Read Sequence/Alignment File Read Sequence Data File Write Alignment File Plot Sequence Viewer Remove Sequence(s)	dseq read   dseq data   dseq write dseq plot dseq remove	Options for manipulating sequence data. Please see the Protein User's Reference Guide for further details.
Save Status		status archive	Saves MSFs and environment (filename.cst) to .tar file. Compresses file to save disk space.
Restore Status		status dearchive	Restores MSFs and previous display conditions.
QUANTA Aliases ->	Define List Delete	alias defi alias list alias dele	Allows user-defined single command alias to replace a series of complex commands.
Record Session ->	Start Stop Suspend Resume	record on record off record suspend record resume	Records all actions during a QUANTA session. Record Session must be off for replay.
Replay Session ->	Start Stop Suspend Resume	replay on replay off replay suspend replay resume	Replays recorded QUANTA session. Record Session must be off for replay.
Log Output ->	Start Stop Suspend Resume	log on log off log suspend log resume	Copies all information in the Textport to a log file.
Open System Window		system	Opens system window from within QUANTA.
Plot Molecules ->	Generate Preview Plot Solid	plot preview plot solid	Generates, previews, and outputs to a file various styles of plot.
X,Y Graphs		xypl	Starts the graph application in a new window.
Restart QUANTA		restart	Closes open MSFs. Copies default .cst file and returns QUANTA to startup conditions.
Exit QUANTA		end	Saves MSFs as necessary and shuts down QUANTA.

Table 30. Edit menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Molecular Editor		3ded	Launches application for building and editing 3D molecules.
Active Atoms ->	All Atoms Remove Solvent Selection Tools	sele chan all all solv sel chan all all noso select palette	Specifies which atoms in an MSF are to be used for modeling operations and calculations.
Select Sets		setd	Changes the current set selection.
Define Dummy Atoms		dummy	Creates and manages dummy atoms to be used in calculations and analysis.
Atom Property Editor		msf table	Edits MSF to change atom names, types, and charges, segment and residue names, and fourth parameter data.
Split and Clean		clean	Allows imported structures to be split according to their molecular type and then have hydrogens added and atom types assigned using appropriate methods.
Apply Dictionary		retype	Reassigns types and charges from a dictionary in QUANTA.
Symmetry ->	Brief Listing Full Listing Define Apply	data symmetry card data symmetry print data symmetry write syms	Defines and manages symmetry. Provides brief and full symmetry information.
Crystal Disorder ->	List Delete Excluded Color Select Label Deassign	diso list diso dele diso excl diso colo diso sele diso labe diso deas	Changes the current crystal disorder selections with select, delete, exclude, color, label, deassign, and list options.
Incorporate Data ->	Fourth Parameter Vectors Charges Show Delete	data incorporate four data incorporate vect data incorporate char data incorporate show data incorporate dele	Reads external data into MSF.
Incorporate Coordinates		msf update	Reads external coordinates into MSF.
Fourth Parameter ->	Edit BValue Occupancy Select Interpretation	edit   set fourth	Selects and edits fourth parameter values including BValue and Occupancy displays.
Atom Data ->	Charge Parameters Type Coordinates, BValue	set charge set param set type edit atom	Edits MSF for atom charge, type, coordinates, BValue, or other atom parameters.
Bond Options		bond algo	Selects bond algorithm and bond display mode for open MSFs.

Table 31. Draw menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Display Atoms ->	All Atoms All Except Solvent Non-Hydrogen Atoms Protein Backbone C-Alpha Trace CA Trace+NonProtein Selection Tools	disp chan all all disp chan all noso disp chan all nonh disp chan all back disp chan all ca disp chan all capl display palette	Defines and manages display options for atoms in open MSFs.
Color Atoms ->	By Element By Segment   By Molecule Selections Tools	colo chan all atom colo change all segm colo diff color palette	Defines and manages color options for atoms in open MSFs.
Property Colors ->	Define Properties Normalization Spectral Colors Electrostatic Colors Toggle Legend Toggle Blended Bonds	prop col prop norm set col spec set col elec prop lege prop blen	Options for coloring structures according to various properties such as thermal parameters or residue position.
Label Atoms ->	Off   Atom Names Atom Type Atomic Charge Residue IDs Residue Name On Selection Tools	label off labe init sel: all end with atnam all end with type all end with char cent resi end with seg resi cent resi end with resn label on label palette	Defines and manages label information for atoms within open MSFs.
Bond Style ->	Half-Bond Vectors Full-Bond Vectors Color by Bond Type Single Vector Bonds Multi-Vector Bonds	bond half bond full bond btyp bond sing bond mult	Selects bonding display style.
Line Style ->	Antialiasing On Antialiasing Off Settings	anti on anti off set style	Selects line style including antialiasing option for bonds.
Manage Display		show	Toggles display lists off and on.
Create Objects		obje create	Creates and manages graphical objects from list of available options.
Object Parameters ->	Mesh Grid Size Ribbon Parameters Brick Map Radius	set grid set ribbon set mapr	Adjusts graphical object parameters such as dimensions and colors for mesh grids, ribbons, and brick maps.
Ruler		obje ruler	Displays a ruler in the viewing area.
Protractor		obje protractor	Displays a protractor in the viewing area.
Solid Models ->	Selection Tools Protein Cartoon van der Waals Ball and Stick Liquorice Redraw Model Settings	solid pal solid chan all secstr solid chan all VDW solid chan all ball solid chan all liqu solid redo solid para	Creates and displays a solid model of a molecular structure as a graphical object or in an external file, depending on system capability.
Ray Trace ->	Original Raytrace Rayshade Solid	rayt rays	Generates renderings of a displayed structure with multiple light sources, shadows, and reflections.
Raster Models ->	Z-buffered Spheres Flat Disk Outlined Disk Smooth Spheres Metallic Spheres Interpenetrating Spheres	raster zbuf raster disk raster outl raster smoo raster meta raster inte	Generates a static space-filling representation of a displayed structure using one of a set of raster image choices.
Dot Surfaces		surf dot	Calculates, displays, and deletes VDW dot surfaces. Not a graphical object.
Captions and Arrows ->	Place Arrow Move Arrow Delete Arrow Delete All Arrows Place Caption Move Caption Delete Caption Delete All Captions	arrow place arrow move arrow remo arrow dele caption place caption move caption remo caption dele	Adds and removes annotations to a molecular display in the viewing area.

Table 32. View menu functions and commands 

Selection	Pull-right selections	Generated Commands	Description
Mono1		view mono	Displays monocular view of molecular structures. Default setting. Toggles with Stereo and Stamp.
Stereo ->a	Crystal Eyes Internal Stereo Side by Side Left Eye View Right Eye View Leeds Viewer Stereo in a Window	view sgraph view istr view stereo view left view right view leeds view swin	Presents stereo view of molecular structures that may be viewed with or without an external device. Toggles with Mono and Stamp. Stereo in a window requires some special setups. See the patches page at the Accelrys website.
Stamp	a	view stamp	Presents all open MSF displays in left-to-right sequence. Does not alter coordinates. Toggles with Mono and Stereo.
Rock ->	On Off	view rock view static	Rocks molecular structures to either side of preselected axis (X,Y,Z) to a predetermined angle limit. Toggles with Roll.
Roll ->	On Off	view roll view static	Rolls molecular structures 360 degrees around predetermined axis (X,Y,Z). Toggles with Rock.
Flash ->	Clock Cycle Off	view flash view flac view stab	Flashes display of molecular structure on and off at predetermined rate.
Settings	aasdfa	set vpar	Sets parameters for Rock, Roll, Stereo, and Flash.
Manage View ->	Orient Save Read Change File	orient view save view read view file	Fixes precise orientations along X, Y, or Z axis. Saves specific transformations and restores previously saved view.
Show Windows ->	All   Palettes Dials Molecule Table Object Table	view pale on, view dial on, show man otab view pal on view dial on show man show otab	Displays one or more standard QUANTA windows.
Hide Windows ->	All   Palettes Dials Molecule Table Object Table	view pale off, view dial off, hide man otab view pal off view dial off hide man hide otab	Hides one or more standard QUANTA windows.
Window Layout ->	Save Current Full Screen Default Screen Saved Screen	wind save wind full wind defa wind reve	Adjusts and saves layout of standard QUANTA windows.
Windows ->	QUANTA Dials Geometry Modeling Molecule Management	TYPE=WINLIST	Allows user to select and bring forward specific window. Window list is context- sensitive, varying with application or function in use.

1 Perspective can be added and removed to stereo viewing using the commands: view pers on/off and can be added to the mono view with the command: view perm and removed with the command: view mono The perspective parameters (eye separation and focal length) can be adjusted using the Dials Emulator Set B.

Table 33. Preference menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Color Definitions ->	All Definitions Blue to Red Red to Blue Black and White Reset Atom Reset All Menu Colors	set color set colo smoo set colo red set colo black set colo atom set colo reset set colo menu	Defines colors applied to atoms and menus.
Bonding Algorithm		bond defa	Defines which bonding algorithm to apply by default to subsequently opened MSFs.
Default Atom Display		set disp	Defines display selection to be applied when MSFs are opened.
Suppress Objects ->	On Off	view suppress on view suppress off	Suppresses object displays until any molecular movement is complete to allow faster manipulations.
ID Mode and Style ->	One ID Only Repick Flashes Repick Deletes ID Style	set id last set id flas set id dele set idst	Selects information included in ID and determines how IDs are displayed.
Output Settings ->	Verbose Messages Normal Messages Terse Messages Textport Paging Echo Commands On Echo Commands Off Confirm Dialogs On Confirm Dialogs Off	set mess verb set mess norm set mess terse set page set echo on set echo off set conf on set conf off	Regulates how much information is supplied to the Textport. The default setting is Normal Messages.
Atom Symbol		set symb	Defines the display of single, non-bonded atoms.
PDB Import/Export		set rename	Options used when PDB files are imported/exported.
MSF Add/Replace ->	Prompt for Options Add to Current Use New MSF only		Controls behavior when a new MSF has been created.
Set MSF Saving Options		set save	Sets MSF saving preferences.
Device Settings ->	Dial Emulators Real Dials Button Box Function Keys Z-Buffer	set dial set knob set butt set func set zbuf	Defines settings for external devices or for keyboard function keys.
Sticky Menus ->	On Off	set sticky on set sticky off	Defines whether menus are allowed to be sticky or not.
All Settings		set	Presents all Preference options including those not listed in the Preference menu.

Table 34. Calculate menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Select Host ->	Solvent Surfaces Interaction Maps CINDO MOPAC UHBD	surf solv host calc prob host exec cindo host exec mopac host uhbd host	Selects host for running any of the calculations listed in the pull-right menu. Allows calculations to be off-loaded to other CPUs.
Retrieve Results		exec retrieve	Examines and retrieves correct results files from a remote host. Automatically copies results files into current local working directory.
Solvent Surfaces ->	Calculate Use Input File Display List Dots	surf solv calc surf solv use surf solv disp surf solv list	Calculates and displays Connolly solvent surfaces.
Solid Surfaces ->	Calculate Calculate Options Re-Display Grid Map	surf soli calc surf soli options surf soli disp surf solid prop	Calculates and displays solid surfaces.
Interaction Maps ->	Probe Molecule Display Map	calc prob calc prom calc prob disp	Calculates and displays empirical energy maps using a probe or a molecule to sample the environment of the displayed structure.
Electrostatic ->	Potential Field	exec vscalc exec field	Calculates electrostatic potential or electrostatic field.
CINDO ->	Calculate Use Input File Read/Display Results	exec cindo calc exec cindo use exec cindo post	Sets up and manages CINDO calculations.
MOPAC ->	Calculate Use Input File Read/Display Results Restart Shutdown Cleanup Files	exec mopac calc exec mopac use exec mopac post exec mopac rest exec mopac shut exec mopac clean	Sets up and manages MOPAC calculations.
UHBD		uhbd	Sets up and manages UHBD calculations.
Hydrogen Bonds		hbond	Sets up and manages calculations and displays of hydrogen bonds.
Dipole Moment		calc dipole	Calculates and displays a dipole moment vector.
Close Contacts		calc contact	Calculates and displays close contacts.
Geometry Monitors		moni	Options for calculating, displaying and listing geometry monitors.
Internal Coordinates   - >	Bonds Angles Dihedrals	calc bond length interactive calc bond angle interactive calc bond dihed interactive	Calculates bond lengths, bond angles, and dihedral angles using selected atoms. Reports results to the Textport.
Vectors and Planes ->	Lines Planes Distances Angles Dihedrals	line plane calc geometry dist calc geometry angle calc geometry dihedral	Calculates vectors and planes between selected atoms.
Coordinate Statistics		calc stat	Calculates minimum, maximum, mean, and standard deviation of molecular coordinates.
Show Status		inqu status	Displays the status of background calculations started by QUANTA.

Table 35. CHARMm menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Select CHARMm Host ->	Interactive Batch NQS	char mach exec batch host exec nqs host	Presents options for running CHARMm calculations.
Initialization Options		char set init	Defines topology and parameter files to be included in charmm.cis. Defines CHARMm output file.
CHARMm Process ->	Initialize Interactive Terminate Interactive Interactive Status Start Batch Job Batch Status Start NQS Job NQS Status	char init char kill inqu stat char exec batch use exec batch stat exec nqs use exec NQS stat	Determines and manages how and where CHARMm runs.
Energy Terms		char set ener	Specifies what energy terms are included in a CHARMm calculation.
Update Parameters		char set upda	Specifies parameters that generally control nonbond terms in CHARMm energy calculations.
Minimization Options		char set mini	Specifies method and parameters to apply in a minimization calculation.
Dynamics Options		char set dyna	Specifies parameters that control a dynamics calculation.
Constraints Options ->	Sel Atom Constraints Atom Constraints On Atom Constraints Off Dihedral/Distance Dihedral On Dihedral Off Distance On Distance Off Stochastic Bdry Settings Stochastic Bdry On Stochastic Bdry Off	char cons atom edit char cons atom on char cons atom off charm cons dihe create charm cons dihe on charm cons dihe off charm cons dist on charm cons dist off charm cons sbound set charm cons sbound on charm cons sbound off	Specifies and manages atom, distance, dihedral, and stochastic boundary constraints during calculations.
SHAKE Options		char set shak	Allows removal of very high frequency vibrations from consideration in dynamics simulations.
Parameters ->	Specify Files Save Parameters Set Options	char read charmm para char set para	Reads, sets, and saves parameter options.
CHARMm Mode ->	PSF RTF MMFF MMFFS PSF Terms RTF Options	charmm mode psf charmm mode rtf charmm mode mmff charmm mode mmffs char set psf char set rtf	Sets PSF or RTF mode and sets specifications for each mode.
Get Fourth Parameter ->	Forces Scalars	charmm get forces charmm get scalars	Retrieves force and scalar data from CHARMm PSF to MSF.
Optimize Hydrogens		char do hbuild	Performs a CHARMm calculation to optimize hydrogen bonds.
Solvate Structure ->	15 Å Radius Sphere 15 Å Length Box 30 Å Length Box Solvate Residues 8 Å Solvate Residues 10 Å 15 Å Methanol Sphere Water Image 15 Å Water Image 30 Å Turn Off Water Image	char do solv 15SP char do solv 15bo char do solv char do solv 8sol char do solv 10sol char do solv spmt char do solv 15on char do solv 30on char do solv off	Adds solvent within specified distances.
Periodic Boundaries		char pbou	Defines a shape matrix for constant pressure dynamics.
Send CHARMm Command		char do comm	Sends CHARMm commands to CHARMm from QUANTA. Initializes QUANTA if it is not already running.
Stream CHARMm File		char do stream	Sends a command directly to CHARMm from QUANTA. Initializes CHARMm if it is not already running.
Capture Commands ->	On Off Suspend Restart	char capt on char capt off char capt susp char capt rest	Captures CHARMm commands sent from QUANTA in a script file that can be reused.
Settings ->	Show Save Restore	char inqu char file save char file chan	Shows current CHARMm setup. Saves or replaces a CHARMm setup file.

Table 36. Applications menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
Builders ->	2-D Sketcher 3-D Builder Sequence Builder Nucleic Acid Builder Solvent/Amorphous Builder	chemnote 3ded sequence build amgr	Launches the 2D or 3D sketchers (ChemNote or the Molecular Editor), the Sequence Builder, or the Nucleic Acid Builder.
Conformational Search		csea	Launches a conformational search.
Molecular Similarity		flexcomp	Launches the molecular similarity application to compare molecular structures.
Analysis		cana	Launches the analysis application.
Dynamics Animation		anim	Launches the dynamics animation application.
Protein Design		prot	Launches the protein design application.
Protein Modeler		pmod	Interface to the MODELER program.
Protein Health		health	Launches the protein health application. Works in conjunction with protein design.
Protein Profile Analysis		prof	Launches the protein profile analysis application. Works in conjunction with protein design.
X-Autofit		xfit	Enters the map skeletonization and chain tracing application.
X-Build		xfit	Enters the X-Ray model building application.
X-Solvate		xsol	Enters the solvent peak search and placement application.
X-Ligand		xlig	Enters the ligand search and placement application.
CNX		xplor	Enters the CNX refinement interface.
Crystal Modeling		xtal	Launches the Crystal Modeling application.

Table 37. Information menu functions and commands 

Selection	Pull-right selections	Generated commands	Description
About QUANTA		about	Provides information about the QUANTA software.
Help...		help help	Starts QUANTA online help.
List Molecule ->	Atoms Residues Bonds Segments Structures Extra Information MSF Titles	list atom list group list bond list segment list molecule inquire extra inq titl	Lists what is active in open MSFs.
Current Selections ->	MSF Atom Display Color Set Label	mole list select list display list color list setd list label list	Lists current selections in the textport.
QUANTA Parameters		list param	Lists atom default parameters in the Textport.
Current Session ->	Mouse Movement Dynamics Parameters Drawing Modes Calculations Constants External Jobs Function Keys Setup Button Box Setup Time and Date User Name	inqu mouse inqu dyna inqu mode inq cons inq stat inqu func inq butt inq time inq user	Provides information in the textport on preferences, selections, and operations in current session.
Command History		inquire history	Lists commands used in current session in textport.