Xsight

Xfit program

Xfit is a molecular modeling and graphics program that is primarily used for fitting and adjusting protein structures to experimental electron density maps. It has a number of features that are useful in the modeling process, for example, skeletonization and pentamer matching. It also has an interactive local refinement capability, and numerous utilities for generating presentation-quality graphics.

The program has a main graphics window called the canvas. The canvas is a window in which all of the molecular and electron density representations are displayed. The canvas is sensitive to mouse events, as described below. In addition to the canvas, there is one main control menu associated with Xfit. This menu gives you full control over all of the various functions within Xfit through a series of additional pop-up menus. It also gives you direct control over manipulation of the canvas window.

Figure 12 . Xfit canvas

Mouse behavior

Mouse events within the canvas have the following effect (MB1 = left mouse button; MB2 = middle mouse button; MB3 = right mouse button).

• MB1: The left mouse button is used to pick or select atoms as well as to rotate the molecule. The act of picking requires a stationary mouse. Click MB1 within the canvas to pick the nearest atom. When an atom is picked, the label will be displayed in the canvas and the atom will be displayed in the Stack window of the main Xfit menu. Click and hold MB1 while moving the mouse to induce rotation of the display. Move the mouse up and down to rotate about the x axis; left and right within the bottom 80% of the screen to rotate about the y axis, and left to right within the top 20% of the screen to perform rotations about the z axis. Warning: If you move the mouse slightly while trying to pick an atom, the event will be interpreted as a rotation request and it will appear as if nothing happened.
• MB1 + <shift>: Clicking and dragging MB1 with the <Shift> key pressed allows you to pan and zoom.
• MB1 + <Ctrl>: Clicking and dragging MB1 with the <Ctrl> key pressed allows you to perform a rotation about the z axis over the whole canvas.
• MB2: The middle mouse button changes purpose depending on the mode that it is in. At start-up time it is in Center mode. This means that if you click and hold MB2 and drag the mouse, the display will translate relative to the center of the canvas. MB2 can also be used to adjust selected portions of the molecule when put into the proper mode. For example, it can be used to adjust torsion angles or translate and rotate selected residues relative to the rest of the molecule. If the mode is different than Center, it will be specified at the bottom right corner of the main Xfit menu.
• MB1 + MB2: If you click and hold MB1 and MB2 simultaneously, and then move the mouse, the effect will be panning and zooming of the display.
• MB3: The right mouse button is used to generate pop-up menus for performing many of the repetitive operations of the fitting process. The default pop-up menu is an icon bar that can be permanently pinned for ready access. The use of the pop-up menu eliminates the constant back and forth motion between the canvas and the main Xfit menu. To pin the menu, first pop it up by clicking and holding MB3. While holding down the button, move the cursor to the pin that is located in the top left corner of the pop-up menu. As soon as the cursor is superimposed on the pin, the pin position will change and you can release the button. The menu will now remain on the screen.

Keyboard shortcuts

Keyboard shortcuts are listed below. Important: these key commands only work when the cursor is in the canvas.

Table 11. Xfit keyboard shortcuts

Key	Function
< i >	zoom in, small increments
< i > + < Shift >	zoom in, large increments
< o >	zoom out, small increments
< o > + < Shift >	zoom out, large increments
< h >	+ rotate around y axis, small increments
< h > + < Shift >	+ rotate around y axis, large increments
< l >	- rotate around y axis, small increments
< l > + < Shift >	- rotate around y axis, large increments
< u >	+ rotate around x axis, small increments
< u > + < Shift >	+ rotate around x axis, large increments
< n >	- rotate around x axis, small increments
< n > + < Shift >	- rotate around x axis, large increments
< j >	+ rotate around z axis, small increments
< j > + < Shift >	+ rotate around z axis, large increments
< k >	- rotate around z axis, small increments
< k > + < Shift >	- rotate around z axis, large increments
< s >	turn off side-by-side stereo
< s > + < Shift >	turn on side-by-side stereo
< esc >	toggle on and off hardware stereo
< r >	rocking off
< r > + < Shift >	rocking on
< x >	view down the x axis
< y >	view down the y axis
< z >	view down the z axis
< + >	add distance cross-bar aid
< . >	remove distance cross-bar aid

The following key commands pertain to the adjusting of torsion angles when only one residue has been selected as active.

Table 12. Xfit torsion angle shortcuts

Key	Function
< 1 >	select 1 as torsion angle to adjust
< 2 >	select 2 as torsion angle to adjust
< 3 >	select 3 as torsion angle to adjust
< 4 >	select 4 as torsion angle to adjust
< 5 >	select 5 as torsion angle to adjust

Floating menu bar

The floating menu bar provides an alternative route for accessing the buttons on the Xfit Main Menu, the MB3 Pop-up Menu and the Expert MB3 Pop-up Menu. These menu items are described below. The floating menu bar also provides the option of changing the XtalView mouse behavior to the Insight II mouse behavior.

Default MB3 pop-up menu

As mentioned above, MB3 can be used to open menus so you can access the most important functions within Xfit without having to take your eyes off the canvas. This can be particularly useful during the fitting procedure.

The default menu is an icon bar that contains 20 different functions:

Figure 14 . Xfit Default MB3 Menu

 

Table 13. Xfit default MB3 menu widgets

Widget	Function
center@	Places a specific atom at the center of the canvas. First, place an atom on the Stack, either by clicking on the atom in the canvas, or by using the Model menu to select the residue and then the atom of interest. In both cases, the selected atom is listed at the top of the Stack in the main Xfit menu. Second, use MB3 to generate the default MB3 menu and select the center@ icon. The selected atom then defines the center of the display.
center	Puts MB2 back into the default center mode, which means that clicking and holding MB2 while dragging the mouse causes a translation of the display relative to the center of the canvas. This is the default mode for MB2 and only needs to be used when one of the other modes has been selected and you wish to return to the default mode. When you select this icon, the label Center Mode is displayed in the bottom right corner of the main Xfit menu.
translate	Once selected, uses MB2 to translate the active portion of the model relative to the rest of the model. The label Move Mode is then displayed in the bottom right corner of the main Xfit menu. This function requires that you select a portion of the displayed molecule as active. The active portion is always highlighted by coloring all of the bonds green.
rotate	Once selected, uses MB2 to rotate the active portion of the model relative to the rest of the model. The label Rotate Mode is displayed in the bottom right corner of the main Xfit menu. This function requires that you select a portion of the displayed molecule as active. The active portion is always highlighted by coloring all of the bonds green.
torsion	Once selected, uses MB2 to rotate torsion bonds within the active portion of the model. Important: you must select the torsion angle to rotate about before the torsion mode becomes active. This function requires that you select a portion of the displayed molecule as active. The active portion is always highlighted by coloring all of the bonds green. The label Torsion Mode is displayed in the bottom right corner of the main Xfit menu only after the angle is selected.   The torsion mode works differently, depending on whether the active portion of your molecule is based on a single residue or on multiple residues. If the active portion is based on a single residue, the torsion angles are selected by pressing keys < 1 >, < 2 >, < 3 >, < 4 >, or < 5 > to select the 1, 2, 3, 4, or 5 angles, respectively. If the active portion is based on multiple residues, the torsion angle must be specified by selecting the two central atoms of the torsion angle.
contour	Contours the region at the center of the display. This function is only useful if contours are displayed. Use this function if you are moving through a structure residue by residue, and want to contour the density as you move the center of the display.
atom	Allows you to select an atom within the model as active by selecting the atom you wish to make active, then selecting the atom icon. Selecting this icon has the same effect as clicking on the Atom button in the main Xfit menu. All bonds associated with the selected atom will turn green. Once active, you can use the translate function to move the atom or the rotate function to rotate it.
atoms	Allows you to designate a set of atoms within the model as active by selecting the atoms you wish to make active, then selecting the atoms icon. Selecting this icon has the same effect as clicking the Atoms button in the main Xfit menu. All bonds associated with the selected atoms will turn green. Once they are active, you can use the translate function to move the atoms or the rotate function to rotate them.
residue	Allows you to designate a residue within the model as active by selecting an atom within the residue that you wish to make active and then selecting the residue icon. All bonds associated with the selected residue will turn green. Once a residue is active, you can use the translate function, the rotate function, or the torsion function to rotate torsion angles. Clicking this icon has the same effect as clicking the Residue button in the main Xfit menu.
residues	Allows you to designate a set of residues within the model as active by selecting one atom from each residue that you wish to make active, and then selecting the residues icon. All bonds associated with the selected residues will turn green. Once the residues are active, you can use the translate function to move them, the rotate function to rotate them, or the torsion function to rotate torsion angles. Selecting this icon has the same effect as clicking the Residues button in the main Xfit menu.
group	Allows you to select part of the model as a group that can be referenced frequently.
molecule	Allows you to designate a molecule within the model as active by selecting an atom from the molecule that you wish to make active, and then selecting the molecule icon. All bonds associated with the selected molecule will turn green. Once a molecule is active, you can use the translate function to move it or the rotate function to rotate it. Selecting this icon has the same effect as clicking the Molecule button in the main Xfit menu.
X (clockwise rotation)	Causes a 90° rotation about the x axis of the screen.
X (counterclockwise rotation)	Causes a 90° rotation about the x axis of the screen in the opposite direction.
Y (clockwise rotation)	Causes a 90° rotation about the y axis of the screen.
Y (counterclockwise rotation)	Causes a 90° rotation about the y axis of the screen in the opposite direction.
Z (clockwise rotation)	Causes a 90° rotation about the z of the screen.
Z (counterclockwise rotation)	Causes a 90° rotation about the z axis of the screen in the opposite direction.
toggle stereo	Toggles the hardware stereo option on and off. It has the same effect as pressing the < Esc > key.
swap	Displays an expert menu the next time MB3 is clicked and held within the canvas. The expert pop-up menu does not contain icons and has much more extensive functionality.

Expert MB3 menu

The expert menu is accessed by first selecting the swap function in the default MB3 menu. Following that, the next time you click MB3 in the Xfit canvas, the expert menu is displayed. The expert menu allows you to access the most important menu functions in Xfit without having to go to the main Xfit menu. In other words, this menu gives you easy and more convenient access to important functions.

The functions available in the expert menu are listed below. If the menu selection has an arrow to the right of it, it is an indication that an additional set of selections is available in an associated menu. With MB3 clicked and held, move the cursor towards the arrow and the menu will appear.

Functions available from the expert menu are listed in Figure  15.

Figure 15 . Xfit Expert MB3 menu

Center at Pick (Expert menu)

The Center at Pick command re-centers the display on the most recently picked atom.

Fit (Expert menu)

You can use the Fit commands to activate portions of the molecule for fitting, and to accept or reject newly fit portions of the molecule.

Figure 16 . Xfit Expert Fit menu

Table 14. Xfit Expert Fit menu widgets

Command	Function
Single Atom	Makes top atom on stack active.
Atoms	Makes all atoms on stack active.
Single Residue	Makes residue associated with top atom on stack active.
Residues	Makes all residues associated with atoms on stack active.
Group	Makes group active.
Molecule	Makes molecule associated with atom on stack active.
Apply Fit	Accepts modified position of active portion of the model.
Reset to Start	Resets active portion of model to starting position but keep active.
Cancel Fit	Resets active portion of model to starting position and cancel active mode.
Undo Last Fit	Nullifies the last Apply Fit command.

Middle Button Mode (Expert menu)

The Middle Button Mode commands allow you to change the behavior of MB2.

Figure 17 . Xfit Expert Middle Button Mode menu

Table 15. Xfit Expert Middle Button Mode menu widgets

Command	Function
Drag Picture	Puts MB2 in Center mode.
Translate	Puts MB2 in Translate mode.
RotateCurrent	Puts MB2 in Rotate mode
Torsion about bond	Puts MB2 in Torsion mode

Clear labels/contacts (Expert menu)

You can use the Clear labels/contacts commands to clean up the display when it is crowded with labels and contact bonds.

Figure 18 . Xfit Expert Clear labels/contacts menu

Table 16. Xfit Expert Clear labels/contacts menu widgets

Command	Function
Clear Labels and Contacts	Removes all atom labels and contact-labeled bonds and labels from canvas.
Clear Labels	Removes all atom labels from canvas.
Clear Contacts	Removes all contact labels and dashed bonds from canvas.

Contour (Expert menu)

You can use the Contour commands to activate map contouring on the canvas.

Figure 19 . Xfit Expert Contour menu

Table 17. Xfit Expert Contour menu widgets

Command	Function
Contour All Maps	Contours all loaded maps.
Contour at Center	Contours map at the center of canvas.
Contour Current Selection	Contours current selected map.

Geometry Refine (Expert menu)

The Geometry Refine menu controls the refinement capabilities of Xfit.

Figure 20 . Xfit Expert Geometry Refine menu

Table 18. Xfit Expert Geometry Refine menu widgets

Command	Function
Pop Start Residue	Uses top atom on stack as starting residue.
Pop End Residue	Uses top atom on stack as ending residue of sequence to be refined.
Setup Refinement	Invokes Setup menu.
Constraints	Invokes Constraints menu.
Refine One Cycle	Performs one cycle of refinement only.
Background Refine ON	Toggles on continuous background refinement.
Background Refine OFF	Toggles off continuous refinement.
Undo Refinement	Returns to starting model.

Setup Refinement

Once you select the residues to refine (Pop Start and Pop End) you can use these commands to set up the residues or to cancel them from refinement.

Figure 21 . Xfit Expert Setup Refinement menu

Table 19. Xfit Expert Setup Refinement menu widgets

Command	Function
Set up refinement residues	Prepares residues to be refined based on sequence defined above.
Clear refinement residues	Clears residues selected for refinement.
Show Geometry	Displays all bond distances for atoms in the refinement residues.

Constraints

This menu allows you to control which atoms will be constrained during refinement.

Figure 22 . Xfit Expert Constraints menu

Table 20. Xfit Expert Constraints Menu Widgets

Command	Function
Constrain atom on stack to screen center	Keeps atom on stack at screen center.
Constrain top two atoms on stack	Prevents the top two atoms on the stack from moving during refinement.
Constrain C-alpha atoms	Constrains C-alpha atoms (useful for refining side-chains).
Restrain Ends	Restrains ends of refinement residues.
Remove constraints on atom on stack	Makes atom on stack available for refinement.
Clear all constraints	Removes all constraints.

Real-Space Refine (Expert menu)

This menu allows you to control features pertaining to real-space refinement.

Figure 23 . Xfit Expert Real-Space Refine Menu

Table 21. Xfit Expert Real-Space Refine menu widgets

Command	Function
Rotamer Search	Adjusts all angles to maximize atom overlap with areas of electron density.
Torsion Search	Adjusts the currently active torsion angle to maximize atom overlap with areas of electron density.
Rotation Search	Rotates the currently active portion of the model about its center of gravity to maximize atom overlap with areas of electron density.
Translation Search	Moves the currently active portion of the model to maximize atom overlap with areas of electron density.

Model (Expert menu)

This menu lets you control features important in fitting residues to electron density.

Figure 24 . Xfit Expert Model menu

Table 22. Xfit Expert Model menu widgets

Widget	Function
Set Insert/ Replace Type	Displays a list of all residue types so you can change the active residue type for either insertion or replacement.
Insert	Activates the Insert menu.
Delete	Activates the Delete menu.

Insert

This menu allows you to control insertion of residues into the model, changing residue type, pentamer searching, and loop searching.

Figure 25 . Xfit Expert Insert menu

Table 23. Xfit Expert Insert Menu Widgets

Widget	Function
Insert After Selection	Inserts a residue (of the type selected with Set Insert/Replace) at the center of the screen; places the residue in the list after the currently selected residue.
Insert Before Selection	Inserts a residue (of the type selected with Set Insert/Replace Type) at the center of the screen and places it in the list before the currently selected residue.
Replace Selection	Replaces the currently selected residue with a residue of the type selected with Set Insert/Replace Type
New model	Places the first residue of a new model.
Pentamers	Activates the Pentamers menu.
Loop Search	Pops up a window that allows you to define a loop search.
Cut Selected into buffer	Loads a list of residues into a buffer. You must first set Residue List to non-exclusive. Then you should select the residues that you want to move. Finally, to make the selected residues disappear, select Cut Selected into Buffer.
Paste buffer before	Places the contents of the buffer before the selected residue.
Paste buffer after	Places the contents of the buffer after the selected residue.

• Pentamers--this menu allows you to fit residue fragments from known protein structures to the structure you are trying to build.

  
  

  Figure 26 . Xfit Expert Pentamers menu

  
  

  Table 24. Xfit Expert Pentamers menu widgets

  Widget	Function
  Find Best Pentamers	Locates the best set of pentamers that fit a sequence of 5 residues, starting with the currently selected residue.
  Cycle Pentamer	Displays the next best pentamer solution.
  Replace Middle 3	Exchanges the middle 3 residues from the 5-residue sequence that was used in the pentamer search with the currently displayed pentamer solution.
  Replace Mainchain Middle 3	Exchanges the middle 3 residues' main chain atoms with the currently displayed pentamer solution.

• Loop Search Window--This menu allows you to generate segments of protein structure using a Monte Carlo conformational search.

  
  

  Figure 27 . Xfit Expert Loop Search window

  
  

  Table 25. Xfit Expert Loop Search window

  Widget	Function
  First Residue	Defines starting residue of loop sequence. You should place a residue on the stack and then click the Pop button to load the residue in this field.
  Last residue	Defines the end residue of the loop region. You should place a residue on the stack and then click the Pop button to load the residue in this field.
  # residues in between	Specifies the number of residues between (but not including) the first and last residues.
  Random Seed	Specifies the number to start the random number generator.
  Search Method	Defines search mode as either random or Monte Carlo based.
  Search for Loops	Starts loop search.
  Cycle Thru Loops	Displays different solutions, once loop search is finished.
  Insert Loop in Model	Inserts currently displayed loop into the model.

Delete

This menu contains commands which allow you to delete or undelete residues from the current model.

Figure 28 . Xfit Expert Delete menu

Table 26. Xfit Expert Delete menu widgets

Widget	Function
Toggle Delete Res Flag	Turns residues on or off for deletion.
Purge Deleted Residues from Model	Removes residues flagged for deletion.

Rotate View 90 (Expert menu)

Provides six icons for 90° rotations in each direction about the three screen axes.

Save Model Being Fit (Expert menu)

This menu provides a quick way to save the current model (and bonds, if you wish) to a .pdb file.

Figure 29 . Xfit Expert Save Model Being Fit menu

Table 27. Xfit Expert Save Model Being Fit Menu Widgets

Widget	Function
Save PDB File	Saves the current model to a PDB format file; requires that a filename be present in the Files menu. (See Files menu.)
Save PDB and Bonds	Saves the current model to a PDB format file and saves bonds to a bond file; requires that a filename be present in the Files menu. (See Files menu.)

Symmetry Atoms (Expert menu)

This menu provides commands that allow you to generate and remove symmetry-related atoms within a particular radius.

Figure 30 . Xfit Expert Symmetry Atoms Menu

Table 28. Xfit Expert Symmetry Atoms menu widgets

Widget	Function
Generate Symmetry Atoms	Creates and displays atoms related by symmetry that are located within the radius specified in the Control menu.
Remove Symmetry Atoms	Removes symmetry-related atoms from the display.

Slab View (Expert menu)

This menu provides you with a convenient tool for changing the slab size in the display.

Figure 31 . Xfit Expert Slab View menu

Table 29. Xfit Expert Slab View Menu Widgets

Widget	Function
Slab In	Decreases the slab thickness.
Slab Out	Increases the slab thickness.
5	Sets the slab thickness to 5 Å.
10	Sets the slab thickness to 10 Å.
15	Sets the slab thickness to 15 Å.
20	Sets the slab thickness to 20 Å.
30	Sets the slab thickness to 30 Å.
50	Sets the slab thickness to 50 Å.

Misc Controls (Expert menu)

This menu contains a number of menus that allow you to control the action of the canvas.

Figure 32 . Xfit Expert Misc Controls menu

Table 30. Xfit Expert Misc Controls menu widgets

Widget	Function
Pick search	Activates the Pick Search   menu.
DrawContacts	Activates the contact toggles.
Mouse Dragging Speed	Controls how large a motion of the display occurs with a given movement of the mouse. Fine indicates a smaller movement and Coarse indicates a larger movement

Pick Search

Figure 33 . Xfit Expert Pick Search menu

Table 31. Xfit Expert Pick Search menu widgets

Widget	Function
Active Model Only	Restricts you to only picking atoms on the canvas that are in the active model.
All Models	Allows you to pick all atoms in all models.

DrawContacts

Figure 34 . Xfit Expert DrawContacts menu

Table 32. Xfit Expert DrawContacts menu widgets

Widget	Function
On	Displays all contacts within the limit set in the Contacts menu when you pick an atom.
Off	Turns contacts display off.

Ridge Lines (Expert menu)

Figure 35 . Xfit Expert Ridgelines menu

 

Table 33. Xfit Expert Ridgelines menu widgets

Widget	Function
Lengthen Color	Extends the coloring automatically through the main chain if you are using the Color Edges mode for the Pick Mode parameter and you are tracing through an apparent main chain region.
Color Side Chain	Colors all of the ridgelines in the sidechain, if you are using the Color Edges mode for the Pick Mode parameter and you are tracing through an apparent side chain region.
Undo Color	Undoes the last coloring operation.
Pick Mode	Selects mode in which objects can be picked. This parameter has three different choices: Models, Edges, and Color Edges. If Models is selected, you will pick atoms from the model if one is read in. The picked atoms will show up in the Stack. If Edges is selected, you will pick ridgelines when you click MB1 in the canvas. The selected ridgeline will appear in the Stack. which can then be used to center the display. If Color Edges is selected, you will pick a ridgeline when you click in the canvas, and it will be assigned a color based on the Color parameter set above.   If you want to color the main chain for a region that looks like alpha helix, select Main as the Color parameter and Color Edges as the Pick Mode parameter. You can then click on each ridgeline in the canvas that appears to be part of the main chain. The color of the ridgeline will change to that of the standard color for Main. You can also use the Lengthen Color from Picked Edge button below to extend a main chain region, once you have picked two ridgelines. Select a ridgeline from each end of an apparent chain and then click the Lengthen Color from Picked Edge button. If you are coloring side chains, you can use the Color Side Chain button to fill out a side chain, once one ridgeline has been selected in the side chain region.

Clear Stack (Expert menu)

Removes all atoms from the stack.

Expand Top 2 on Stack (Expert menu)

This command selects all residues between the top two residues listed on the stack.

Toggle Stereo (Expert menu)

Toggles hardware stereo on and off.

Swap Menu (Expert menu)

Toggles back to the default icon menu--this only takes effect the next time you want to open a menu with MB3.

Main Xfit menu

The main Xfit menu contains a number of buttons along the top that are used to access additional menus or perform specific functions. If a button title is followed by ellipses (...), it is associated with additional menus or pop-up windows. A summary of each widget function follows. In addition, detailed descriptions of each supplemental menu can be found starting at Xfit supplemental menus.

Figure 36 . Xfit Main menu

Table 34. Xfit main menu widgets

Widget	Function
Quit	Exits the Xfit program. Note that you are not prompted to save the current model.
Files	Xfit can read in a number of different types of files. Files can be specified when the program is started or they can be specified and read using the Files menu.
Ridgelines	Loads or saves GRINCH-style files containing information about skeletonization. You enter the name of the file in the text field and then click the Load or Save buttons. The default extension for the GRINCH-style files is .bones (see Ridgelines menu).
LSQ Fit	Superimposes two models or portions of models by least-squares fitting. This can be useful in comparing the overlap between two models (for example, before and after a refinement), and it can also be used in fitting known structural motifs or fragments to a roughly fit model (see LSQ Fit menu).
Canvas	Toggles between the accelerated canvas and a PostScript preview canvas.
PostScript Preview Canvas	Gives a good representation of what a PostScript display will look like.
CX Canvas (SUN only)	Shows the default drawing canvas.
View	The View menu has a number of functions that save and control the view of the display. In addition, this menu controls stereo viewing, as well as functions pertaining to creating Vu objects (see View menu).
Show	Displays a menu for controlling which objects are displayed in the canvas window. Also controls the blinking object option (see Show menu).
Colors	Displays a menu for modifying object and background colors (see Colors menu).
FFT	Displays a menu of Fourier calculations you can perform, based on an assortment of coefficients. The and Fc values can either be from an existing .phs file or newly generated from the SFCalc menu (see FFT menu).
Plot	Displays a menu that allows you to set plot file parameters for PostScript files.
Refine	Displays a menu that allows you to perform real-space refinement for fitting individual residues to the density maps. Also allows you to perform reciprocal space refinement for overall geometry refinement.
Control	Displays a menu which allows you to tailor various parameters to match the performance of your system, since software performance is related to your hardware. Also controls a number of display characteristics (see Control menu).
Contours	Displays a menu (see Contours menu) which controls the size, level, and color of displayed electron density grids.
Model	Displays a menu (see Model menu) which selects atoms and residues as "active". This is an alternative method to selecting "active" atoms and residues by clicking on them in the canvas graphics window. In addition, you can use this menu to fit residues to electron density maps.
SFCalc	Displays a menu (see SFCalc menu) which calculates structure factors either by an FFT method or by standard summation. When coupled with the FFT routine, XtalView has a compete set of tools for on-line structure factor and Fourier calculations.
Labels	Displays a menu (see Labels menu) which modifies the position and content of atom labels. This facility is mostly used to change the position and color of particular labels in presentation graphics.
Crystal	Displays the current crystal file. A different crystal file can be selected by typing in the name or using the associated button menu.
Cell	Displays the unit cell parameters from the current crystal file. Modifying the parameters has no effect. If the cell parameters must be changed, you must go back to Xtalmgr and change the crystal file, or go back to Insight II and use the Utilities/Crystal command within the Xsight module.
Front Clip	Defines the upper limit in z, expressed in units of Å. It is difficult to focus on a particular region of a structure if the full depth of the structure is displayed at once. For this reason, only atoms that fall within a certain range of the coordinate z are usually displayed at one time (the z axis is perpendicular to the screen).
Back Clip	Defines the lower limit in z, expressed in units of Å.
Slab	Defines the total range of the displayed structure expressed in units of Å. The slider allows you to select the magnitude of the slab as a fraction of an upper limit. To change the upper limit, click on the associated menu button with MB3 and select the desired value.
Stack	Lists atoms that are selected from the canvas graphics window or from the Model menu. These atoms can then be used for stack-based operations such as centering or distance calculations.
Clear Labels	Displays a menu used to clear the canvas graphics window of labels and/or distances. Clicking the button with MB1 performs the default operation of Clear Labels and Contacts, while clicking the button with MB3 displays the menu of three clear commands.
Clear Labels and Contacts	Removes all atom labels, distance labels, and contact lines from the display.
Clear Labels	Removes all atom labels from the display.
Clear Contacts	Removes all distance labels and contact lines from the display.
Clear Stack	Removes all atoms from the stack.
Expand Top 2	Selects all residues between the top two residues listed in the stack.
Delete	Removes an individual atom from the stack if you first select the atom from the Stack list, and then click the Delete Item button.
Distance	Calculates distances when you place two atoms on the stack and click this button. Distance labels are drawn in the canvas window by default. In addition, they are listed in the scroll window at the bottom of the main Xfit menu.
Angle	Calculates angles when you place three atoms on the stack and click this button. Angles do not get labeled in the display and are only listed in the scroll window at the bottom of the main Xfit menu.
Torsion	Displays a menu for calculating torsion angles. Clicking the button with MB1 performs the default operation of Calculate torsion angle for top 4 on stack, while clicking the button with MB3 displays the list of two torsion commands.
Calculate torsion angle for top 4 on stack	Calculates the torsion angle when you place four atoms on the stack and click this button to calculate the torsion angle. Torsion angles are not labeled in the display, and are only listed in the scrolled window at the bottom of the main Xfit menu.
Show Torsions of Current Residue	Displays a small menu that contains numeric fields for all of the torsion angles for a residue. A residue must be selected as current (highlighted in green) to use this option. If the model is manipulated, the torsion angles are updated in the menu automatically.
Bonds	Draws a bond between the top two atoms in the stack.
Break Bond	Deletes the bond between the top two atoms in the stack.
Fit Model #	Allows you to move between models using the arrow boxes. Multiple models can be loaded into Xfit.The currently active model always is drawn with brighter colors.
Fit	Selects portions of a model for manipulation. The portion of the model selected for manipulation is considered active. To activate a portion of the model you must first select an atom or atoms, by picking from the canvas graphics window or using the Model menu. You then select one of the Fit buttons: Atom, Atoms, Residue, Residues, Group, or Molecule. The active portion of the model turns green within a few seconds to indicate what you have selected. For example, if you want to activate three sequential residues, you would first place one atom from each residue on the stack and then click the Residues button.
Surface	Displays a van der Waals surface for the active atoms. You have a choice of using a standard van der Waals radius or twice the van der Waals radius.
Density	Controls the density of the dot surface. If the Surface option is activated, the van der Waals radius (or two times the van der Waals radius) is represented by dots drawn at the specified distance from the active atoms. Some portion of the molecule must be active for this option to work.
Reset	Restores the geometry to the original position if a portion of the molecule has been activated, and if the activated portion has been modified from its original position. The activated portion of the model remains active after pressing the Reset button.
Cancel	Restores the geometry to the original position and deactivates the model--if a portion of the molecule has been activated, and the activated portion has been modified from its original position.
Apply Fit	Replaces the original position of the active portion of the molecule with the modified position--if a portion of the molecule has been activated, and the activated portion has been modified from its original position. The activated portion of the model deactivates after pressing the Apply Fit button.
Symm Atoms	Toggles symmetry-related atoms on or off. Clicking the button with MB1 performs the default operation of Generate Symmetry Atoms, while clicking the button with MB3 presents a list of two symmetry commands.
Generate Symmetry Atoms	Generates all symmetry-related atoms within a specified radius of each atom in the model. The symmetry-related atoms are included in the display with all atoms of a specific molecule represented by the same color. The radius used in the calculation is modified in the Control menu with the Symm radius parameter. It is not the purpose of this command to generate full symmetry-related molecules, but rather to show the packing environment of the model within a certain distance from the surface
Remove Symmetry Atoms	Removes the atoms generated by Generate Symmetry Atoms from the display.
Contour	Controls contouring. Clicking the button with MB1 performs the default operation of Contour All Maps, while clicking the button with MB3 presents a list of three contour commands.
Contour All Maps	Contours all currently loaded maps.
Contour at Center	Contours the currently active map at the center of the screen. (The currently active map is listed at the top of the Contour menu.)
Contour Current Selection	Centers the contours about the currently active portion of the model.
SAVE	Saves the model. Using MB1 to click the button performs the default operation of Save PDB File, while using MB3 to click the button presents a list of the two save commands.
Save PDB File	Saves the current model to a .pdb file. You must enter a file name in the Output PDB parameter of the Files menu before you can save a file.
Save PDB and Bonds	Same as above, except that bonds are saved in a file that has the same name as the .pdb file but an extension of .bond. Contains one record for each bond. Each record consists of the two integers that correspond to the atom numbers of the bonded atoms.
Swap	Toggles between the fit model and the unfit model. The unfit model that you wish to toggle between is selected using the Select Save Set menu button. Each time you select a portion of the model to fit, the old positions are saved in one of 20 save sets. If you click on the Apply Fit button and accept the modified model, the unmodified model is stored in one of the 20 save sets and you can access it later if you need to. This allows you to undo any of the last 20 fitting actions.
Select Save Set	Lists all of the save sets from previous fitting operations and selects one for swapping. The label of a save set indicates the last residue in the selected model and the total number of atoms involved in the fitting operation.

Xfit supplemental menus

This section provides detailed descriptions of the menus described in the previous section (Main Xfit menu).

Files menu

Files can be loaded into Xfit either as arguments on the command line when first starting the program, or through the Files menu. If you load files on the command line, you must use proper file extensions. In contrast, if you use the Files menu, you may load files that do not conform to the conventions of the XtalView file extensions.

The Files menu is composed of a file filter, a directory specifier, and file reading and saving facilities for each of the file types. In addition, it includes a directory browser and a file browser to help find files.

Figure 37 . Xfit Files menu

Ridgelines menu

This menu gives you the flexibility to color a ridgeline file created from Xskel. A ridgeline file is essentially a file of connected lines or vectors that trace the regions of electron density. You can color the different lines depending on what part of the structure you think they represent. Initially the lines are unassigned and they all appear as the "unknown" structure type (gray). However, as you look at the lines and start to recognize secondary structural features, you can color the different regions to help emphasize the differences. The structure will start to become recognizable as you assign colors to the different areas.

Figure 38 . Xfit Ridgelines menu

LSQ Fit menu

It is often useful to look at differences between models, in order to evaluate the progress of a structure refinement, or to compare a newly fit C trace with known structural fragments such as -helices and -sheets. The LSQ Fit menu can be used for both types of calculations. You must specify the source model that will be least-squares fit to the target model.

Figure 39 . Xfit LSQ Fit Menu

Table 37. Xfit LSQ Fit menu widget

Widget	Function
Source--Model #	Specifies the Source model by #. The #'s and file names of the current models are listed in the Show menu. You can use the arrows to select the appropriate model #, and the model name is simultaneously displayed.
Start at Residue Name	Selects the starting residue for the sequence of residues to be fit. Draws the names of the selected residue and atom on the display and also lists them in the stack window of the main menu. You must first select an atom from the residue and place it on the stack (use the mouse in the canvas, or use the Model menu). Then you click the Pop button to load the residue name.
Pop	Loads the selected residue number into the Start at Residue Name numeric field.
Chain ID	Specifies chain ID, if defined.
Group #	Specifies group number, if defined.
Target--Model #	Specifies the Target model by #. The #'s and file names of the current models are listed in the Show menu. You can use the arrows to select the appropriate model #, which simultaneously displays the model name.
Start at Residue Name	Selects the starting residue for the sequence of residues to be fit. Draws the names of the selected residue and atom on the display and also lists them in the stack window of the main menu. You must first select an atom from the residue and place it on the stack (use the mouse in the canvas, or use the Model menu). Then you click the Pop button to load the residue name.
Pop	Loads the selected residue number into the Start at Residue Name numeric field.
CHain ID	Specifies the chain ID, if defined.
Group #	Specifies the group number, if defined.
Match Atom Types	Indicates what atom types to use in the least-squares fit, for example, N, CA, CB. If you do not specify an atom type, all atom types are fit.
Length of Match	Specifies the number of residues in the source model to be matched. If this option is used, you must set the Fit Source Residues option to For Length Only.
Fit Source Residues	Fits all of the residues in the source model to the target model (All in chain) or specifies a number of sequential residues to fit (For Length Only). The number of sequential residues is specified in the Length of Match numeric field.
Draw Arrows	Represents the degree of overlap between two models by arrows, whose ends are attached to the source atoms, and whose heads are pointing in the direction of the related target atoms. The relative magnitude of the distance between two related atoms is represented by the length of the arrow. These arrows are drawn if the Draw Arrows check box is selected.
Scale	The Scale slider controls the absolute length of the arrows that are drawn between related source and target atoms, if the Draw Atoms option is selected. The units of the scale slider are arbitrary, and the slider position should be selected based on a value that gives a reasonable view.
Least Squares Fit	This button executes the least-squares fitting based on the menu selection of the user.
Undo Last Fit	The last least-squares fit can be nullified by clicking this button.
AutoFit	This option is not currently available.

View menu

The View menu is used to save a particular view, modify a view, create editable script files that describe the view, generate stereo renderings, and create alternative representations of the model (vu objects).

The top of the menu contains the geometrical information necessary to reconstruct the current view: the coordinates for the center of the display, the orientation matrix, and the zoom value. These numbers reflect the values of the display before the View button was clicked. You can modify the values for Center, Matrix, or Zoom, by entering the desired numbers and pressing the Set View button. The current values of Center, Matrix, and Zoom can be updated in the menu by clicking the Get View button.

The view is stored as a series of XtalView script commands and a number of options are available for manipulating these script commands. The script commands for rotation are the same as used by the program MOLSCRIPT (Kraulis 1991).

Figure 40 . Xfit View menu

Table 38. Xfit View menu widgets

Widget	Function
Center	Specifies the coordinates for the center of the display.
Matrix	Specifies the rotation matrix necessary to generate the view.
Zoom	Specifies the zoom distance.
Get View	Sets Center, Matrix, and Zoom values, based on the current display.
Set View	Sets display, based on Center, Matrix, and Zoom values.
File	Specifies the *.script file to be loaded or saved.
Load	Retrieves saved view files with .script extensions.
Save	.Saves the current view as a *.script file.
Edit Script	Provides you with an editor to modify an existing .script file. Clicking MB3 while the cursor is in the edit region displays a menu with four options, each of which has an additional pop-up menu.
Make Script	Generates the appropriate script commands to display the current view and places them in a text editor. You have the same editing options described above. You must save the file using the option Store as New File.
Plan View	Splits the viewing area into the standard viewpoint in the bottom half of the screen, and a from-the-top view in the top half of the screen. This is useful for docking operations as you can see and control all three axes and translations at once. This feature is not available on all display devices or in all display modes.
Hide H's	Turns Hydrogen atoms on and off in the display.
Split Stereo	On generates a split screen stereo display. Left and Right generate left- and right-eye views only for making hardcopy drawings or slides. Hardware supports "Crystal Eyes" and "StereoVision" glasses on SGI workstations. Hardware stereo can be toggled off with the Off button. Hardware stereo can also be toggled on and off with the <Esc> key.
Separation	Adjusts the separation of the split stereo view, although a better way to change the separation is to adjust the width of the display window by selecting and dragging the vertical window border.
Angle	Makes the split stereo view either cross-eyed or wall-eyed.
Make Vu Object from Model #	Selects the number of the model to be used to generate the Vu object.
First Res	Specifies the first residue. You can load a residue to the stack by selecting it in the graphics window using the mouse, and clicking the pop button.
pop	Loads the first residue number, based on the top residue of the stack.
Last Res	Specifies the last residue. You can load a residue to the stack by selecting it in the graphics window using the mouse, and clicking the pop button.
pop	Loads the last residue number, based on the top residue of the stack.
Chain ID	Selects a sequence of residues that share the same chain ID.
Atom Filter	Sets an atom filter to select a subset of atoms for the Vu object. Enters a list of atom names, separated by spaces, e.g., C N CA O. An asterisk can be used as a wildcard and thus C* would imply C, CA, CB, CG1, etc. CG* would match CG1, CG2, etc.
Res Type Filter	Sets up a residue filter to select a subset of residues for the Vu object. Residue names must be three letters, capitalized, and separated from each other by spaces.
Include	Generates subsets of atoms using the appropriate check boxes: main chain atoms (C, N, CA, O), CA's only, non-protein atoms, and side-chain atoms. In addition, displays peptide planes and H-bonds.
Coloring	Colors Vu objects. There are three options: Solid (makes all items in the Vu object the same color), C* only (makes all C atoms in the Vu object the same color), or Bvalue (varies color as a function of the B factor). It is useful to display the Color menu when performing this operation, so you can see or change the currently selected color.
Vu number	Increments each time a new Vu object is created. You can overwrite an existing Vu object by decrementing the Vu Number.
Make Vu	Generates and displays a Vu object with the selected characteristics. By default, the Vu object has the same contents as the model file from which it is generated. To hide the model and only display the Vu object, you must use the Show menu.
PhiPsi Plot	Generates a Ramachandran phi-psi plot based on the current model. When you generate a phi-psi plot, you are prompted as to whether you want to add "bad" phi-psi values to the error list. If you answer yes, you are presented with a list of the bad phi-psi values. Clicking on one of the values automatically positions the C atom of the offending residue in the middle of the screen. In this way, you can easily examine the outliers. The plot will be sent directly to a printer or saved as a PostScript file. To print, enter the name of the printer in the Printer/File text field and then press the Print button.To save as a PostScript file, enter the filename in the Printer/File text field and then click the Print button with MB3. A pull-down menu appears that contains the option of printing to a PostScript file. The plot characteristics can be changed by pressing the Properties button with MB3 and pinning the menu to the screen. Individual characteristics can then be changed by entering a numeric value in the numeric field next to the Properties button and pressing the appropriate button in the properties menu.
B-Value Plot	Generates a B-value Plot based on the current model. By default, the plot is sent directly to a printer when you enter the name of the printer in the Printer/File text field and click the Print button, but you can also save it as a PostScript file by entering the file name in the Printer/File text field and clicking the Print button with MB3. A pulldown menu appears that contains the option of printing to a PostScript file. The plot characteristics can be changed by clicking the Properties button with MB3 and "pinning" the menu to the screen. Individual characteristics can then be changed by entering a numeric value in the numeric field next to the Properties button, and pressing the appropriate button in the Properties menu.
Max B	Sets the maximum B value for the B-value plot, which can be adjusted to prevent any bad temperature factors from ruining the scaling of the plot.

Show menu

Objects can be hidden by deselecting them in the scrolled lists that are available in this menu. Useful information about each object is given to help identify them. An object that is difficult to identify can often be found by toggling it on and off. To speed up rotation, hide all objects that are not needed.

Figure 41 . Xfit Show menu

Table 39. Xfit Show menu

Widget	Function
Models	Displays a scrolled list of loaded .pdb files, displays model files by default. To remove a model from the display, de-select it by clicking on the appropriate entry in the scrolled list.
Maps	Displays a scrolled list of .phs files. If an FFT calculation has not yet been performed, a file indicates "0 lines" and is not selected for display. To add or remove a map from the display, select or de-select the appropriate file.
Vu Objects	Toggles vu objects created in the View menu on or off using the scrolled list.
Clear Contacts	Removes all contacts drawn because the Draw Contacts option was selected in the Control menu.
Clear Labels	Removes atom labels drawn on the display.
Set Blink Group 1	The Blink Group buttons set up two groups of Vu objects that can be displayed in an alternating or blinking fashion. The blinking frequency is set by the Blinking Rate slider in the Control menu. Set Blink Group 1 establishes the first grouping of objects when you first select all of the objects you want in the first group, and then click the Set Blink Group 1 button.
Set Blink Group 2	Establishes the second grouping of objects. You should de-select the objects from group 1 (unless a particular object is desired for both groups) before you select the objects for group 2.
Blinking	Activates and deactivates blinking

Colors menu

Xfit uses a default color scheme for different atom types, that is, carbon is yellow, nitrogen is blue, oxygen is red, hydrogen is white, iron is brown, and sulfur is yellow. The Colors menu allows you to modify the color of models, vu's, the background area, the current atoms, and symmetry-related atoms.

Four shades of each possible color are displayed in the Colors menu. The different shades are used to give the effect of depth-cueing. These colors are defined and stored in the $XTALVIEWHOME/data/colors.dat file.

Select a color by clicking on it. For any particular color, it does not matter which of the four boxes you click on; color shades are only displayed for reference.

Figure 42 . Xfit Colors Menu

Table 40. Xfit Colors menu widgets

Widget	Function
Color Model	Changes the color of the carbon atoms (set Color Style to C* atoms) or all of the atoms in a model (set Color Style to All Atoms), based on the model and color style you have selected. When you click the desired color, select the desired Color Style and then press the Color Model button. It is not possible to change the color of the other elements.
number	Specifies the model number. If multiple models are loaded into Xfit, the model number can be selected with the adjoining arrow boxes.
Color Style	Specifies the color style (CA only in all atoms).
Color Vu	Modifies the color of Vu objects. This is done by picking the desired color in the color table and then selecting Color Vu. When the Vu object is first created (from the View menu), you may select a single color for the whole Vu object (Solid), maintain different colors for different elements (C* only), or set colors based on the variation in atomic temperature factors (Bvalue). Once the Vu object is created, it is only possible to change the overall color of the object. If you create multiple Vu objects, you select a Vu object for display using the arrow boxes adjoining the Vu number.
number	Specifies the Vu object to color.
Color Bkgnd 1	Defines one of two background areas in the canvas graphics window. Background 1 occupies the bottom 80% of the window and defines the area of the canvas window in which horizontal MB1 mouse movements result in y rotations of the model.
Color Bkgnd 2	Occupies the upper 20% of the background and defines the area in which horizontal MB1 mouse movements result in z rotations of the model.
Color Current 1	Displays atoms that are selected as "current" in the color of your choice. "Current" atoms are displayed in a different color to help distinguish what is active for fitting.
Color Current 2	Colors bonds that exceed an acceptable length.
Color Symm Atoms	Colors symmetry-related atoms the color of your choice.

FFT menu

This routine provides a fast way of calculating electron density maps. Although it is possible to read pre-calculated electron density map files into Xfit, it is more convenient to generate electron density internally using the FFT menu. It is actually faster to calculate the maps internally than to read pre-calculated maps, and you can redefine the grid size, resolution limits, and grid size at any time.

The FFT menu is automatically displayed if a .phs file is read into Xfit.

Figure 43 . Xfit FFT menu

Table 41. Xfit FFT menu widgets  

Widget	Function
Map #	Specifies the map number. You can calculate different maps and differentiate them by number. The different maps can be toggled on and off in the Show menu. To calculate multiple maps, it is necessary to load a .phs file for each new map, even if you want to use the same .phs file.
Title	Specifies the .phs file from which the map is calculated.
nx, ny, nz	Designates the frequency of grid points along the a, b, and c axes. These parameters must be even. Three times the maximum h, k, and l values usually give a good map representation. Each index maximum can be estimated from: (cell edge) / dmin which is how the default nx, ny, and nz parameters are selected. Increasing the number of grid points makes a smoother density surface but degrades rotation performance.
Min Resolution	Sets minimum resolution of the data to be used in the Fourier calculation.
Max Resolution	Sets maximum resolution of the data to be used in the Fourier calculation.
Coefficients	Displays a menu which lets you select the appropriate Fourier coefficients.
Apply	Starts the Fourier calculation based on the menu parameters, and displays the map in the canvas window.

Refine menu

The Refine menu is divided into two areas: rigid fragment real space refinement and geometry refinement. In real space refinement, you select the map against which you want to refine, then you maximize the atom/density overlap using four different types of searches. With geometry refinement you can either refine the positions of individual atoms in the whole molecule or in a portion of the molecule.

Figure 44 . Xfit Refine menu

Table 42. Xfit Refine menu widgets

Widget	Function
Map #	Specifies the map used to refine the model in real space. The arrow boxes can be used to select the desired map.
Rotational Search	Refines the currently selected portion of the model in a rotational sense, to maximize the overlap between atoms and electron density.
Translational Search	Refines the currently selected portion of the model in a translational sense, to maximize the overlap between atoms and electron density.
Rotamer Search	Refines the currently selected residues using a torsion angle search of the side chains, to maximize the overlap between atoms and electron density.
Torsion Search	Refines the currently selected torsion angle to maximize the overlap between atoms and electron density. This option requires that you first select the torsion angle. If a single residue is currently active, then you can select torsion angles by first clicking and holding MB3 while the cursor is in the canvas graphics window. Next you select the Torsion icon. The 1, 2, 3, 4, or 5 torsion angles are activated by pressing the <1>, <2>, <3>, <4>, or <5> keys respectively. If multiple residues are currently active, the desired torsion angle must be specified by picking the two central atoms of the angle. The atoms attached to the second of the picked atoms are the ones then refined.
Update R-density while fitting	Displays the R-density in the bottom left corner of the canvas graphics window. If you are manually adjusting the torsion angles, the value is updated as the torsion angle is changed.The R-density is a value related to the maximum overlap of atoms and electron density. The largest value relates to the best overlap.
Start at Residue	Specifies the starting residue (and chain ID, if defined) for a sequence of residues to refine. You must first place an atom from the residue on the stack, and then click the pop button.
Chain ID	Specifies chain identifier.
End at Residue	Specifies the ending residue of a sequence to be refined.
Chain ID	Specifies chain identifier.
Refine while fitting	Three options are available. You can turn refinement off. You can refine continuously (Always). Or, you can refine only if triggered by a user-induced movement (Events Only).
Refine Against Map	Specifies that refinement will occur against the displayed map.
Set Up Refinement Residues	Displays a menu that controls refinement.
Set up refinement residues	All residues in the sequence for refinement. You must set up the starting and ending residues before selecting this option.
Clear refinement residues	Clears residues that have been selected for refinement.
Show Geometry	Displays distances during refinement.
Refine	Starts refinement of selected sequence.
Constraints	Specifies refinement constraints.
Constrain atom on stack to screen center	Constrains atom at top of stack to center of the screen.
Constrain top two atoms on stack	Constrains top two atoms on the stack during refinement.
Constrain C-alpha atoms	Prevents movement of CA atoms during refinement.
Restrain Ends	Prevents movement of end atoms.
Remove constraints on atom on stack	Removes stack constraints.
Clear all constraints	Clears all constraints that have been set.
Distance	Specifies distance for the top two atoms on the stack.
Sigma	Specifies the sigma of the distance between the top two atoms on the stack.
Heat	Not implemented at this time.
Bond Weight x 10	Specifies a portion of the weighting scheme for refinement.
Angle Weight x 10	Specifies a portion of the weighting scheme for refinement.
Plane Weight x 10	Specifies a portion of the weighting scheme for refinement.
Map Weight x 10	Specifies a portion of the weighting scheme for refinement.
Number Cycles	Specifies the total number of cycles (only used if you refine while fitting is off).
Errors	Generates a menu with all errors.
Verbose output	Generates detailed output.

Control menu

This menu contains parameters for tailoring the performance of Xfit to the hardware platform and also controls some of the display characteristics.

Figure 45 . Xfit Control menu

Table 43. Xfit Control menu widgets

Widget	Function
Mouse Damping	Controls the relative relationship of cursor movement to display motion. The number of pixels the cursor moves translates into a certain number of degrees of rotation in the display. The largest ratio of pixels/degrees is obtained if the Mouse Damping slider is positioned to the extreme left. This results in very fine movements of the display for large cursor movements.
Draw Mode	Provides two drawing modes and an additional option for removing map grids during the motion of the display. The Fast mode refreshes the screen for every event. The Jerky mode skips to the end of the event queue, if the workstation cannot keep up with the motion events. In spite of the name, this mode provides the most pleasing effect on an SGI workstation. The Skip Contours mode removes the map grids from all translation and rotation events, and only redisplays the map grids once the motion has stopped. If a large number of vectors are being drawn, the performance of your workstation can be degraded by rotation and translation operations.
Model Pick	The default setting for this parameter (Active Model button) allows only picking of atoms in the currently "active" model. You select the "active" model in the main Xfit menu using the Fit Model # parameter. If you select the All Models mode, the closest atom from any model is activated by clicking in the graphics display. The Model Pick parameter is useful if more than one model is loaded into Xfit. If symmetry related atoms are added to the display, they are treated as an additional model and the All Models mode must be selected in order to pick them.
Label Picked Atoms	Draws the label in the vicinity of the selected atom, which is "picked" in the graphics display window (see Model Pick above). If this parameter is toggled off, "picked" atoms are not displayed in the graphics display window, although the selected atom names still appear in the Stack list of the main Xfit menu.
Symm radius	Controls the search radius (in Angstrom units) for adding symmetry-related atoms, when these atoms are added to the display using the Symmetry Atoms button, located on the main Xfit menu.
DepthCue (% front)	Specifies the relative brightness front to back.
Rocking	Introduces animation of the display. Initiation of this option results in the display rotating back and forth about the vertical axis through a specified angular range and a specified speed.
Rocking Rate	Controls the relative speed of rotation of the display via a slider.
Rocking Range	Controls the specified angular range of rotation of the display.
Blinking Rate	Controls the speed of blinking as defined in the Show menu (see Show menu)
Draw Distances	Calculates and displays distances between two atoms in the canvas graphics window, when you first select two atoms (with the mouse or by using the Model menu), and then click the Distance button located in the main Xfit menu. You can control whether distances are drawn in the canvas window. The distance also appears in the scroll window of the main Xfit menu, making it unnecessary to clutter the drawing with distances. If you wish to remove distances which have been drawn on the screen, use MB3 to click the Clear Labels button (in the main Xfit window) and select the Clear Contacts option.
Draw Contacts	Draws contacts between atoms. This parameter has three settings: Off, All, and Inter-residue. When the All setting is selected and an atom is subsequently picked, a line and distance are drawn between the picked atom and every atom that is within the Contact Search Radius. The Inter-residue setting does not draw contacts between atoms of the same residue. If you wish to remove distances which have been drawn on the screen, use MB3 to click the Clear Labels button (from the main Xfit window) and select the Clear Contacts option.
Contact Radius	Defines the search radius (in units of Angstroms) for finding short contacts, in conjunction with the Draw contacts parameter.

Contours menu

Contours describe iso-value surfaces in a three dimensional electron density map. Five different iso-value surfaces can be displayed simultaneously in Xfit. The Contours menu gives you control over the sigma level and the color of each iso-value surface as well as the size of displayed map. Each map is scaled so that 1 is equal to a value of 50. None of the changes made to this menu actually take effect until the Apply button is clicked.

Figure 46 . Xfit Contours menu

Table 44. Xfit Contours menu widgets

Widget	Function
Map #	Allows you to choose the map whose parameters you wish to modify, since Xfit has the capability of displaying multiple maps. A specific map can be addressed by typing in the number associated with the map, or by using the arrow boxes to select the proper number. The file name associated with each map (either a .phs file if the map was calculated internally or a .map file if the map was calculated external to Xfit) is displayed and it is possible to modify the name of the file by clicking the Rename button.
Rename	Modifies the name associated with the map within Xfit, but does not rename the file at the UNIX level.
Contouring Method	Supplies four different modes of displaying contours. The cube mode displays density as a cube with a specific radius. The sphere mode displays density as a sphere with a specific radius. The Different Axes mode displays density as a parallelepiped (defined by a, b, and c axes below), and the Blob mode displays density as spheres around active atoms.
Cube/Sphere Radius	Defines the electron density as a box that encloses a sphere of the specified Radius in angstroms, if set to the Cube contouring method. Thus, to increase the size of the displayed density region, increase the value of the radius.
Max	Sets the maximum cube/sphere radius on the slide-bar.
A Axis, B Axis, C Axis	Defines the dimensions (in Angstroms) for the Different Axes mode of the Contouring Method.
Extend Blob Around Current Atoms by	Displays electron density around selected atoms by the radius (in angstroms) defined here.
1, 2, 3, 4, and 5	Allows modification of each of the five iso-values as to the level, the color, and whether or not it will displayed. The maps are scaled so that a value of 50 in the map is equal to 1 . The default contour levels for the 5 iso-values are 1, 2, 3, 4, and 5 respectively. You can change the level for any one of the iso-values by typing in a value in the numeric field or by using the associated slider. None of the modifications made in this menu take place until the Apply button is clicked.
Set to Current Color Level	Sets the color of the selected iso-value. To change the color of an iso-value, click Colors in the main Xfit menu, and click the desired color of an iso-value. Then go to the Contour menu, and click the number of the iso-value in the Set to Current Color Level parameter. This updates the Color parameter for the selected iso-value, but the color of the contour does not change until the Apply button is clicked.
Styles	Five different pre-defined styles of iso-value display are provided with the Styles menu button. Clicking on the Styles menu button with MB3 displays a list of styles. Selecting the desired style automatically loads it into the menu.
Average over Non-Crystallographic Symmetry	Displays averaged electron density if a non-crystallographic symmetry axis has been identified and the matrix is stored in the crystals file.
Auto Contour on Scroll	When this option is set on (default), electron density maps are automatically re-contoured around the center of the display when the display is translated by more than half the width of the window.
Apply	Updates the electron density display based on any changes you have made to the menu. In addition, if the center of the display has changed since the last time the density was updated, the density is centered at the new position.

Model menu

This menu gives you control of the currently active model on both the residue level and the atom level. Model is used in de novo model fitting, as well as in changing residue types of known models. The currently active model is defined by the Fit Model # parameter located in the main Xfit menu.

Figure 47 . Xfit Model menu

SFCalc menu

This menu allows you to calculate structure factors in a variety of ways. In addition, gradients of the difference density can be calculated for each atom and represented by an arrow.

Figure 48 . Xfit SF Calc menu

Table 46. Xfit SFCalc menu widgets

Widget	Function
Model #	Selects the model to be used in the structure factor calculation by clicking on the arrow boxes.
Map #	Selects the .phs file to be used as a source of reflections by clicking on the arrow boxes.
d max	Specifies the largest d value to be used in a structure factor calculation.
d min	Specifies the smallest d value to be used in a structure factor calculation.
Calculate All and Scale	Recalculates all of the structure factor amplitudes and phase angles, and calculates a scale factor between the calculated and observed data.
Omit Current Atoms	Calculates the structure factor contributions from atoms that are currently selected (highlighted in green), and then subtracts them from the existing structure factors. The scale factor is not recalculated. Use this option when calculating OMIT maps.
Update Current Atoms	Modifies the calculated structure factor amplitudes and phase angles based on the currently selected atoms. In other words, if a residue has been selected for fitting and it has been moved relative to its starting position, this calculation modifies the existing structure factor amplitudes and phase angles for this one residue only. It does this by first subtracting the contribution of the residue in its original position and then adding the contribution in the new position.
Method	Calculates structure factors either by an FFT method or a summation method. The FFT method is much faster than the summation method, unless only a few residues are involved.
Auto FFT after calculation	Calculates FFT automatically after the structure factor calculation.
Shake to reduce phase bias	Slightly modifies all atoms using a random number generator to remove phase bias.
Deriv vu number	Specifies the .vu file. The results of a derivative difference map calculation is a .vu file that contains arrows originating on each atom. Its magnitude indicates the steepness of the gradient, and the direction of the arrows indicates the direction in which the atom would want to shift in a refinement. Use the arrow boxes to change the number of the .vu file. By default, the number is incremented each time you run the calculation, but you might prefer to overwrite an existing .vu file, and that would require decrementing the counter.
Sign of Delta	Determines the direction of the derivative arrows, either by Fo-Fc or Fc-Fo.
Scale Arrows x 100	Sets an arbitrary scale for the length of the derivative arrows.
Derivatives of Current Atoms	Initiates the calculation of derivatives of the difference map. It requires that atoms, a residue, multiple residues, or a molecule be currently active for the calculation to take place. At the end of the calculation, the derivative arrows are displayed in the canvas window in the form of a .vu file. That .vu file can be toggled on and off using the Show menu.

Labels menu

This menu allows you to modify labels that appear in the canvas graphics window. All of the labels that are currently displayed in the canvas window are listed in a scrolled list at the top of the menu. New or modified labels use the current color, so it is useful to activate the Color menu when performing label manipulations.

Figure 49 . Xfit Labels menu