xleap is a windowing interface to LEAP. In
addition to the command-line interface contained in
the Universe Editor window, it has a Unit Editor
(graphical molecule editor), an Atom Properties
Editor, and a Parmset Editor. These editors are
discussed in subsequent subsections.
The window that first appears when the user starts xleap is
called the Universe Editor. The Universe Editor is the most
basic way in which users can interact with xleap. It has two
parts, the "command window," which corresponds to the tleap
command interface, and the "pulldown" items above the window,
which provide mouse-driven methods to generate specific commands
for the command window, either directly or via popped-up dialog
boxes. Within the command window, the user can cut and paste
text using the mouse buttons:
LEFTBUTTON-
Begin selection.
RIGHTBUTTON-
Continue selection.
MIDDLEBUTTON-
Append the selection to the last input line.
The command window has a scroll bar that allows the user
to scroll back and review messages that have scrolled off
the top of the window.
Because some commands within LEAP can be very long,
the command window allows users to spread input for single
commands over multiple lines. A block is defined as one or more lines of
input that contain a single command and all of its arguments.
LEAP uses two criteria to determine whether a line terminates a block.
- ·If the last character in a line is a backslash
then the block is continued on the next line.
- ·If the block has any open lists, meaning if there are more "{"
(open lists) than "}" (close lists), then the block will continue
to grow in lines until all lists are closed. This is to facilitate
entry of LEAP commands that use long lists as arguments (e.g., the
zMatrix command). Note: from this it follows that, if typing
many carriage returns seems to have no effect, an extra open left-hand
brace is the probable cause.
The items in the pulldowns allow the user to generate
commands using dialog boxes. To display the "File"
pulldown, for example, press the left mouse button
on "File;" to select an item in the pulldown, keep
the button down, move the mouse to highlight the item,
then release the mouse button.
A dialog box will then pop up containing fields
which the user can fill in, and lists from which values
can be chosen; these will be used to generate commands
for the command window interface.
Currently, the following pulldown/popup commands are defined:
loadOff-
The dialog box contains a single file list.
The user can move about the subdirectories
and select the desired LEAP OFF library to load.
Alternately, the name of the file to be
loaded may be typed. The user should press the "Accept"
button after selecting a file in order to execute
the command.
saveOff-
This dialog box contains a list of UNITs/PARMSETs and
a file list. The user must choose the UNIT or
PARMSET to save, and choose the file to which to write.
If the file to be written to does not exist, the
user may type the name of a new file into the
file name text box. The user can enter the
command by pressing the "Accept" button.
loadAmberPrep-
The dialog box contains a single file list.
The user can move about the subdirectories,
and select the AMBER PREP file to load.
Alternately, they may type the name of the file to be
loaded. The user should press the "Accept" dialog box
button after selecting a file.
loadPdb-
There are two parts to this dialog box.
The PDB file will be read into a UNIT
and that UNIT will be associated with a
variable. The variable name to associate with
the UNIT is entered into the first text field.
The name of the PDB file is either selected
from the file list or the file name is typed into the dialog box.
The user can execute the command by pressing
the "Accept" button.
impose-
This dialog box has three parts. The first part is
a list of UNITs from which the user can select the
UNIT which is to be changed. The second part is a
list of STRING objects that may or may not contain
internal coordinates. The third part is a text field
for entry of RESIDUE sequence numbers, or ranges of
sequence numbers. The user executes the command by
pressing the "Accept" button.
edit-
A list of UNITs and PARMSETs that can be edited is
presented to the user. The user may select one
or type in the name of a UNIT. The user may "Accept"
or "Cancel" the command by pressing one of these two buttons.
source-
The user can select a file which is to
be used in a source command from the file list.
Alternately, they may type the name of the file to be
loaded. The user should press the "Accept" button after
selecting a file.
verbosity-
The user is presented with three levels of
verbosity in order to regulate the amount
of output to be displayed during the LEAP
session. The user should select one
of these verbosity level buttons and
press the "Accept" button to enter the command.
quit-
The user may "Accept" or "Cancel" the quit command.
When the user enters the edit command from the
Universe Editor Command Window, the Unit Editor will
be displayed if the argument to the edit command
is an existing UNIT or a nonexistent (i.e. new) object.
The Parmset Editor will be activated if the argument
is a PARMSET. The Parmset Editor is discussed
later in this subsection.
The Unit Editor has five parts. At the top of the window is a
pulldown menu bar; below it is a set of buttons titled
"Manipulation" that define the mode of mouse activity in
the graphics window, and below that, a list of elements
to select for the manipulation "Draw" mode (selecting one
automatically selects "Draw" mode). Then comes the graphical
molecule-editing ("viewing") window itself,
and at the very bottom a text window where status and errors
are reported.
The menu bar has three pulldowns: "Unit," "Edit," and "Display."
Unit pulldown
The Unit pulldown contains commands affecting the whole UNIT.
- "Check unit" - checks the UNIT in the viewing window for
improbable bond lengths, missing force field atom types, close
nonbonded contacts, and a non-integral and non-zero total
charge. Information is printed in the text window at the bottom
of the Unit Editor.
- "Calculate charge" - the total electrostatic
charge for the UNIT is displayed in the text window at the bottom
of the Unit Editor.
- "Build," "Add H & Build" - the coordinates of new atoms
are adjusted according to hybridization (inferred from bonds)
and standard geometries. (See also the
Edit pulldown's "Relax
selection.) Newly-drawn ATOMs are marked as "unbuilt" until
they are marked otherwise by one of the Build commands or
by the Edit pulldown's "Mark selection (un)built."
The builder only builds coordinates for unbuilt ATOMs.
This allows users to draw molecules piecemeal and make adjustments
as they draw, without worrying that the builder is going to undo
their work. "Add H & Build" adds hydrogens to the ATOMs that do
not have a full valence and builds coordinates for the hydrogens
and any other ATOMs that are marked "unbuilt." The number of
hydrogens added to each ATOM is determined by the hybridization
and element type of each ATOM.
- "Import unit" - a selection window pops up for the user to
incorporate a copy of another unit in the current one. The
imported unit will generally superimpose on the existing one.
(Hint: select all atoms in the current unit before doing this
to simplify dragging them apart using the Manipulation
Move mode.)
- "Close" - Exit the Editor.
Edit pulldown
The Edit pulldown contains commands relating to the currently-
selected ATOMs in the viewer window. Selection is described
below in the "Manipulation buttons" section.
- "Relax selection" -
performs a limited energy minimization of all
selected ATOMs, leaving unselected ATOMs fixed in place, by
relaxing strained bonds, angles, and torsions. If atom types
have been assigned and can be found in the currently-loaded
force field, force field parameters are used.
If no types are available then default parameters are used
that are based on ATOM hybridization. This command invokes
an iterative algorithm that can take some time to converge
for large systems. As the algorithm proceeds, the modified
UNIT will be continuously updated within the viewing window.
The user can stop the process at any time by placing the
cursor within the viewing window and typing
control-C.
Since only internal coordinates are energy minimized,
steric overlap can result.
- "Edit selected atoms" -
pops up an Atom Properties Editor, a tool for examining/setting
the properties of the selected ATOMs. The Atom Properties Editor
allows the user to edit the ATOM names, types, charges, perturbed
names, etc. in a convenient table format. It is described in
a separate section below.
- "Flip chirality"
This command inverts the chirality of all selected ATOMs.
In order for the chirality to be inverted, the ATOM cannot
be in more than one ring. The operation causes the lightest
chains leaving the ATOM to be moved so as to invert the
chirality. If the ATOM has only three chains attached to it,
then only one of the chains will be moved. Note: this
command is rather apt to crash LEAP.
- "Select Rings/Residues/Molecules" - expands the currently
selected group of atoms to include all partially-contained
rings, residues, or molecules.
- "Show everything" - causes all ATOMs to become visible.
- "Hide selection" - makes all selected ATOMs invisible.
- "Show selection only" - makes only selected ATOMs visible.
- "Mark selection unbuilt/built" - see "Unit/Build," above.
Display pulldown
The Display pulldown contains commands that determine
what information is displayed within the viewing window.
- "Names" - toggles display of ATOM names at each ATOM position.
- "Perturbed names" - toggles display of perturbed ATOM names.
The perturbed names are displayed immediately after the
unperturbed names and are prefixed with a forward slash "/".
(See the "Concepts" section for a discussion of Free Energy
Perturbation ATOM names.)
- "Types" - toggles display of molecular mechanics atom types.
The ATOM types are displayed within parentheses "()".
- "Perturbed types" - toggles display of perturbed atom types
of the ATOMs. Perturbed types are displayed
within the same parentheses as the unperturbed
types, immediately after the unperturbed types, and
are prefixed by a forward slash "/".
(See the "Concepts" section for a discussion
of Free Energy Perturbation ATOM types.)
- "Residue names" - toggles display of residue names.
These are displayed at the position of the first ATOM,
before any of that ATOM's information that may be displayed.
The residue names are displayed within angled brackets "<>".
- "Axes" - toggles display of the Cartesian coordinate axes.
The origin of the axes coincides with the origin of Cartesian space.
- "Periodic box" - toggles display of the periodic box,
if the UNIT has one.
The Manipulation buttons are Select, Twist, Move, Erase, and Draw.
They determine the behavior of the mouse left-button
when the pointer is in the Viewing Window.
Select-
This button allows one to select part or all of a UNIT in anticipation
of a subsequent operation or action. In the Select mode, the user can
highlight ATOMs within the viewing window for special operations.
The cursor becomes a pointing hand in the viewing window in this mode.
Selected ATOMs are displayed in a different color (or different line
styles on monochrome systems) from all other ATOMs. Atoms can be
selected with the left-button in several ways: first, clicking on an
atom and releasing selects that atom. Clicking twice in a row on an
atom (at any speed) selects all atoms (this is a bug - only the
residue should be selected). Keeping the button down and
moving to release on another atom selects all ATOMs in the shortest
chain between the two ATOMs, if such a chain exists. Finally, by first
pressing the button in empty space, and holding it down as the mouse is
moved, one can "drag a box" enclosing atoms of interest. Note that a
current selection can be expanded by using the "Edit" menubar pulldown
select options to complete any partial selection of rings, residues or
molecules. menu options within the Selection menu.
- If the user holds down the SHIFT key while performing any
of the above actions, the same effect will be seen, except
ATOMs will be unselected.
Twist-
Twist mode operates on previously-Selected atoms.
The intention is to allow rotation about dihedrals; if
too many atoms are selected, odd transformations can occur.
While in the Twist mode, the pointer looks like a curved arrow.
Twisting is driven by holding down the left-button anywhere
in the viewing window and moving the mouse up and down.
Move-
Like Twist, Move mode operates on previously-Selected
atoms. While in the Move mode, the pointer looks like four arrows
coming out of one central point. Holding down the left-button anywhere
allows movement of these atoms by dragging in any direction in the viewing
plane. (The view can be rotated by holding down the middle-button to allow
any movement desired.) This option allows the user to move the selected
ATOMs relative to the unselected ATOMs.
To rotate the selected ATOMs relative to the unselected ones,
press and drag the mode (left) button while holding down the SHIFT key.
The selected ATOMs will rotate around a central ATOM on a "virtual sphere"
(see the section below on the rotate (middle) button for more information on
the "virtual sphere"). The user can change which ATOM is used as the center
of rotation by clicking the mode (left) button on any of the ATOMs in the
window.
Erase-
Erase mode causes the cursor to resemble a chalkboard
eraser when it is in the viewing window. Clicking the left-button
will delete any atoms or bonds under this cursor, one atom
or bond per click.
Draw-
Choosing Draw is equivalent to choosing the
default "Elements" atom in the next array of buttons;
the initial default is carbon. While in the draw mode,
the pointer is a pencil when in the viewing window.
Clicking the left-button deposits an atom of the current
element, while dragging the cursor with the left-button
held down draws a bond: if no atom is found where the
button is released, one is created.
- When the pointer approaches an
ATOM, the end of the line connected to the pointer will
"snap" to the nearest ATOM. This is to facilitate drawing
of bonds between ATOMs. Any bonds that are drawn will by
default be single bonds. To change the order of a bond,
the user would move the mouse to any point along the bond
and click the mode (left) button. This will cause the order of the
bond to increase until it is reset back to a single bond.
The user can cycle through the following bond
order choices: single, double, triple, and aromatic.
- If the user rotates a structure as it is being drawn, she
will notice that all of the ATOMs that have been drawn lie
in the same plane. New ATOMs are automatically placed in
the plane of the screen. The fact that LEAP places the
new ATOMs in the same plane is not a handicap because once a
rough sketch of part of the structure is compete, the user can invoke
one of LEAP's two model building facilities ("Unit/Build" and
"Edit/Relax Selection" in the Unit Editor Menu bar) to build
full three dimensional coordinates.
C, H, O, ...-
These buttons put the viewing window in Draw
mode if it is not in that mode already, and select
the drawing element. The more common elements have
their own buttons, and all elements are also found
by pulling down the other elements button.
The viewing window displays a projection of
the UNIT currently being edited. The user
can manipulate the structure within the
viewing window with the mouse. By moving the
mouse and holding down the mouse buttons, the
user can rotate, scale, and translate
the UNIT within the window. The functions attached
to the mouse buttons are:
Rotate (Middle button)-
By pressing the rotate (middle) button within the
viewing window and dragging the mouse, the
user can rotate the UNIT around
the center of the viewing window. While the
rotate (middle) button is down,
a circle appears within the viewing window,
representing a "virtual sphere trackball."
As the user drags the mouse around the
outside of the circle, the UNIT will
spin around the axis normal to the screen.
As the user drags the mouse within the circle,
the UNIT will spin around the axis in
the screen, perpendicular to the movement
of the mouse.
The structures that are being viewed can be
considered to be embedded within a sphere
of glass. The circle is the projection of
the edge of the sphere onto the screen.
Rotating a UNIT while the mouse is within the
circle is akin to placing a hand
on a glass sphere and turning the sphere by
pulling the hand. The rotate operation does not
modify the coordinates of the ATOMs; rather,
it simply changes the user's point of view.
Translate (Right button)-
By pressing the translate (right) button within the
viewing window and dragging the mouse around
the viewing window, the user
can translate the UNIT within the plane of
the screen. The structures will follow the
mouse as it moves around the window. This
operation does not modify the coordinates of
the UNIT.
Scale (middle plus right button)-
If the scale "button" (holding the middle
and right buttons down at the same time) is
depressed, the user will change the size of the
structures within the viewing window. Pressing
the scale (middle plus right) button
and dragging the mouse up and down the screen will increase
and decrease the scale of the structures. This operation
does not modify the coordinates of the UNIT.
Mode button (left button) and the viewing window mode-
The function of the left button is determined by the current
mode of the viewing window as described in the "Manipulation"
section, above. When the mouse enters the viewing window it
changes shape to reflect the current mode of the viewing window.
Spacebar-
Another always-available operation when the pointer is in the
viewing window is the keyboard spacebar, which centers the view
of the molecule, and is especially useful if the UNIT becomes
"lost" due to some operation.
The functions of the middle and right buttons are fixed
and always available to the user. This allows the user to
change the viewpoint of the UNIT within the viewing window regardless
of its current mode. The user might ask why there are controls to translate
in the plane of the screen, but not out of the plane of
the screen. This is because LEAP does not have depth-cueing
or stereo projection and this makes it difficult
for users to perceive changes in the depth of a structure.
However, the user can rotate the entire UNIT by 90 degrees which
will orient everything so that the direction that was coming out
of the screen becomes a direction lying in the plane of the screen.
Once the UNIT has been rotated using the rotate (middle) button, the
user can translate the structure anywhere in space. While
it does take some getting used to, users can
become very adept at the combination of rotations and
translations.
The Atom Properties Editor is popped up by the Unit Editor
when the user selects the Edit selected atoms command
from the Edit pulldown. The Atom Properties Editor
allows the user to edit the properties of ATOMs using
a convenient table format. ATOM properties are:
name, type, charge, element, perturbed name,
perturbed type, and perturbed charge. (Mass is
not perturbed.)
The Atom Properties Editor has three parts: the
Menu Bar, Status Window, and Table Window.
The Menu Bar has two pulldowns: Table and Operations.
Table-
"Save" - save current table.
This transfers the properties in the table to
the ATOMs. The table is first checked, and if
something is incorrect, a warning box
pops up with the option to cancel the save.
- "Save and quit" - save current table (as in "Save")
and quit.
- "Close table" - the table information is discarded
and not applied to the ATOMs. If the table has been
changed, a warning box pops up with the option to
cancel the close.
Operations-
"Find..." - pops up a dialog box to enter a string
to search for. All fields in the table are searched,
and if the string matches the contents of a field,
that cell is highlighted.
- "Find next" - find next instance of current search
string.
- "Check table" - check each field in the table for
errors. Error information is printed in the Status
Window. The first error in the table is highlighted.
- "Go to next error" - highlight the next error from
the last "Check table" command.
The Status Window is used to display messages from the
Atom Properties Editor.
The Table Window contains the properties of the selected ATOMs
in the UNIT. The properties can be edited by clicking the mouse
left-button in a cell (clicking again to position the cursor
within an existing string), and typing/backspacing to modify
the contents. Also, a selection can be made by dragging the
cursor with the left-button down, then pasted into other cells
by positioning the cursor over the target cell and clicking
the middle button.
The ATOM properties are:
Name-
This is a case-sensitive STRING.
The names for all ATOMs in a RESIDUE should be unique.
The name has no relevance to molecular mechanics
force field parameters; it is chosen arbitrarily as a means to
identify ATOMs. Ideally, the name should correspond to
the PDB standard, being 3 characters long except for hydrogens,
which can have an extra digit as a 4th character.
Type-
This is a STRING property.
It defines the force field atom type. It is important
that the character case match the canonical type definition
used in the appropriate "parm.dat" or "frcmod" file.
For smooth operation, all atom types need to have
element and hybridization defined by the addAtomTypes
command. The standard AMBER force field atom types are
added by the default "leaprc" file.
Charge-
This property is the monopole atomic charge centered on the ATOM.
See the Appendices for more information on deriving these charges.
The value can be any floating point number
(e.g., 3.0, -1.0E-2).
Element-
The atomic element provides a simpler description of the
atom that the type, and is used only for LEAP's
internal purposes (typically when force field information
is not available). The element names correspond to standard
nomenclature; the character "?" is used for special cases.
The element name is automatically generated when drawing
new atoms.
Perturb-
This is a flag that indicates whether to consider the
ensuing perturbation information when building a perturbation
topology file using the saveAmberParmPert command.
The setting is "true" if the ATOM is to be perturbed, nothing
or "false" otherwise. Unless one is setting up a perturbation,
this aprt of the table can be ignored.
Perturbed name-
This property is a case-sensitive STRING. The
property is a unique identifier for an ATOM in
its final state during a Free Energy Perturbation
calculation. LEAP fills in the unperturbed name
as a default. The perturbed name has no effect
on calculations and is mainly useful as a reminder of
what was intended.
Perturbed type-
This property is the force field atom
type of the perturbed species in a Free Energy
Perturbation calculation. The atom type is
used to assign force field parameters. The type
can be any string from the force field.
Perturbed charge-
This property is the monopole charge on an ATOM
at the completion of a Free Energy Perturbation
calculation. The value can be any
floating point number (e.g., -1.0E-2, 3.0).
If the user enters the command edit Foo in the
Universe Editor and Foo is a PARMSET,
then a Parmset Editor is popped up. First, a
window appears which contains a number of
buttons. The buttons list the parameters that can
be edited - Atom, Bond, Angle, Proper Torsion, Improper
Torsion, and Hydrogen Bond - and an option to close
the editor. Choosing one of the parameter buttons
will pop up a Table Editor. This editor resembles
that of the Atom Properties Editor, having three parts:
the Menu Bar, Status Window, and Table Window.
The Menu Bar has three pulldowns: Table, Edit and Operations.
Table-
"Save" - save current table.
This transfers the parameter definitions in the
table to the PARMSET. The table is first checked,
and if something is incorrect, a warning box
pops up with the option to cancel the save.
- "Save and quit" - save current table (as in "Save")
and close the Parmset Editor.
- "Close table" - the table information is discarded
and not applied to the PARMSET. If the table has been
changed, a warning box pops up with the option to
cancel the close.
Edit-
"Add row at end" - create a new, empty row at the end of the table.
- "Insert row before selection" - insert a new, empty row before the
row containing the currently-selected cell.
- "Delete row" - delete row containing currently-selected cell.
Operations-
"Find..." - pops up a dialog box to enter a string
to search for. All fields in the table are searched,
and if the string matches the contents of a field,
that cell is highlighted.
- "Find again" - find next instance of current search string.
- "Check table" - check each field in the table for
errors. Error information is printed in the Status
Window. The first error in the table is highlighted.
- "Go to next error" - highlight the next error from
the last "Check table" command.
The Status Window is used to display messages from the
Parmset Editor.
The Table Window contains the parameters in a table format.
The cell that is currently being edited is highlighted;
clicking mouse left-button over a cell selects it.
[Contents] [Previous] [Next]
Updated on January 5, 2000. Comments to case@scripps.edu