Alter

The ``Alter'' menu contains sub-menus for altering the display characteristics of many of spock's objects.  

Bonds

  Sets the display characteristics for displayed bonds. For the purposes of coloring, each atom ``owns'' half of the bond, so the bond color will change halfway between the connected atoms to the new atom's bond color (settable via the bc command, §5.2.1, § 5.2.1). Both the primary and secondary bond drawing mode are controlled by this menu. (Bonds with a negative color are rendered in the secondary bond mode see §5.2.1).

• Lines: simple lines connecting the bonded atoms.
• Cylinders: cylinders connecting the bonded atoms. This displays faster than the capped cylinders.
• Capped Cylinders: cylinders connecting the bonded atoms, with rounded caps on the ends.
• Sticks: A four-sided representation of the bond. This helps to give a sense of perspective, and is faster than the cylinders.
• Ball and Stick: cylinders connecting atoms, with spheres at the atom positions. The spheres are twice the bond radius.
• Ball to stick ratio: When displaying bonds in ball-and-stick mode, this parameter determines the ratio of the ball size to the stick size.
• Radius Entry: Requests the radius of the cylinders (and width of the sticks) to be used. Be warned: unlike the Control Panel (§6.1.8), there is no maximum radius here. Caveat ussor.
• Thick line bonds: By default line bonds are one pixel wide. Toggling this option makes them two pixels wide.
• No hydrogen: This option toggles inclusion of hydrogen atoms in bonds. If it is turned on, bonds to or from hydrogen atoms are not drawn. This makes it easier for many people to look at structures which have hydrogen atoms. The difference between this command and a bc=0,element=1 command is that that command would only hide bonds from hydrogens. There would still be a half-bond to the hydrogen with that command.
• No half bonds: Turning on this option disables half-bond representations entirely. Recall a colored atom is bonded to an atom with bc=0, by default there is a half-bond to the non-colored atom. This option turns off half bonds.
• Edit Bond Material: A short cut to the bond material editor. See §6.11.4.

   

Atoms

    This menu controls the display characteristics of atoms. For speed, the default mode for atoms is a flat representation. This can be changed to a more traditional representation. The resolution can be changed via the ``Sphere Resolution Entry'' option. However, when the molecule is actively being rotated or translated, the resolution for most modes temporarily drops down to a level consistent with fast drawing. In all cases, the radius of the atomic representation is taken from the atomic radius and may be changed via the set radius= command (§ 5.2.4).

• Solid Spheres: A solid spherical representation.
• Line Spheres: A wire-frame spherical representation. This is very slow to draw on most hardware, and should probably not be during active manipulation of the view.
• Point Spheres: A ``dot'' representation of the sphere. The dot density may be changed via the ``Sphere Resolution''.
• Circles: The default ``flat'' representation. Obviously, this one's for speed, not for looks.
• Texture-mapped: This representation looks 3-dimensional, but is actually not. A single image of a sphere is read in and used as a texture map which is applied to all atoms. The appearance is much better than the flat circles, and the performance is much better than solid spheres on hardware with accelerated texture-mapping. This is a nice compromise between the solid and flat representations. For presentation graphics you should still use the solid spheres.
• T-Mesh Spheres: This is a toggle for the rendering style of spheres. Using this representation may take slightly longer than the to calculate initially, but later redraws are much faster, so this on by default.
• Sphere Resolution Entry: Sets the resolution of the sphere. The maximum value is hardware-dependent. The higher the resolution, smoother the appearance of the sphere, and consequently the more time it takes to draw. This parameter is also accessible via the Control Panel (§6.1.8).
• Edit Atom Material: A short cut to the atom material editor. See §6.11.4.

   

Worms

  This menu controls the display of the ``worm'' backbone representations. By default, worms are built for all molecules, through the CA's of proteins and the phosphorus atoms of nucleic acids. If you wish to add additional worms, however, you may do so. Note that worm types other than Tubular and Variable Radius expect all backbone atoms. Attempting to use other worm types with CA-only structures will result on a Tubular worm.

For nucleic acids, the worm type defaults to rectangular, and the ``rectangular helix'' properties defined below are used. Also note that if your nucleic acid structure has non-standard bases in it (e.g. inosine), that the default definition will skip those bases. You may change the definition under the ``Build worm'' menu option to a=_P__, which should ignore the residue type.

• Build Worm: This allows the user to provide a selection string which will be used to build a new worm. The user is first asked if they wish to keep the old worms. Answering ``yes'' will cause the new definition to be appended to the previous list of worms. A ``no'' response will overwrite all previously defined worms. For details on how to provide a selection string, see §5.3. The initial selection string is ``{a=_ca_&&r=aa}||{a=_P__&&r=dna}''.
• Tubular: This type of worm is has a circular cross section, which is perpendicular to the direction of travel of the chain.
• Oval: This type of worm is has a oval cross section, which is perpendicular to the direction of travel of the chain, oriented so that the long axis of the ellipse is in the plane of the peptide bonds.
• Rectangular: This type of worm has a rectangular cross section, oriented so that the plane of the rectangles matches the plane of the peptide bonds. For DNA and RNA, the results are undefined. Note that there is a shadow color for the narrow edges of the rectangles, this color can be changed as described in § 5.2.1.
• Stranded: This produces a ribbon of five simple lines. Again the orientation of this ribbon is through the plane of the peptide bonds.    
• Secondary structure: This is the most informative of the representations. Helical residues are represented by wide regions with an elliptical cross section, and sheets are represented by rectangular regions with arrow heads at the C terminal end. Coils and turns are both represented by thin tubular regions. The determination of what residues belong to what secondary structural type is taken from the `` structure'' atomic property, and may be changed via the `` set structure'' command described in § 5.2.4, or may be automatically assigned from DSSP output as described in §6.1.1 and 6.7.8.

  NOTE: if the structure ends in a -strand ordinarily the arrowhead would look truncated, because the two terminal sections of a worm are only half as long as the rest. As this looks odd, I have decided that in this special case, the arrow head will actually be made up of parts of two amino acids. A necessary side effect of this is that if the arrowhead residue and the residue immediately N-terminal to it are not the same color, the arrow head will be two different colors. If you don't like the way this looks, you must color both terminal residues the same color.

• Variable Radius: This worm also has a circular cross section. However, the width of the worm is taken from one of the atomic property arrays (ap2 or the atomic B-factor by default). The widths are normalized so that the segment with the highest value is twice the normal worm radius, and the segment with the lowest value is one tenth the normal radius.    
• Thin ribbon: This representation is much like the stranded representation above, except that it consists of filled polygons. This ribbon is a good compromise between appearance and speed, as it has the speed of the stranded ribbon, and a good appearance. This ribbon is also ideal for exporting to VRML (§ 6.1.2), as it consumes the fewest resources of all the representations. This representation turns on the ``Tie Faces'' option for worms (§6.11.5).
• Edit worm parameters: This option pops up a dialog box where you can edit the parameters used in the construction of the worms. These parameters give the user a large degree of control over the appearance of worms, particularly the secondary structure worms.
  • Lengthwise resolution: the number of worm segments per residue. By default, it is 4 for all worms except rectangular (20), and secondary structure (10). For the rectangular and secondary structure worms, the defaults are minimum values.
  • Crosswise Resolution: the number of vertices in a cross section of the worm, 10 by default.
  • Strand smoothing steps: the number of times to smooth the CA coordinates when drawing strands in the secondary structure drawing mode. If you want the stands to follow the oscillations of the CA's, set this to 0.
  • Gap Distance: the maximum allowable gap before a break will be inserted in the worm. The default (around 8 Ångstroms) is appropriate for normal proteins and most DNA. Some RNA structures may require a higher setting.
  • Base width/radius: This is the width of the worm in Ångstroms. Actually it's the half-width, but who's counting? For variable width worms, this serves as the radius of a worm segment that's halfway between the maximum and minimum values.
  • Standard height factor: For ``oriented'' worms which are wider in the plane of the peptide bond, this factor is multiplied by the base width to get the height of the cross section. Only the round and variable radius worm styles are not ``oriented''.
  • Standard width factor: As above, this factor is multiplied by the base width to get the width of the cross section.
  • Helix height/width factors: These are height and width factors (like the standard ones above) that are applied only to helices in the secondary structure representation, and to DNA/RNA worms.
  • Coil radius factor: The multiplication factor for the coil/turn regions of a secondary structure worm.
  • Arrow base width: This is multiplied by the base radius to form the bottom of arrowheads on strands in the secondary structure worms.
  • Arrow tip width: This is multiplied by the base radius to form the top of arrowheads on strands in the secondary structure worms.
  • Cardinal spline tightness: This parameter is used in the calculation of the cardinal spline. It should range from 0.0 to 1.0 with 1.0 producing more rounded splines and 0.0 producing very angular splines. The default is 0.5. For more rounded looking helices, try 0.75. If you adjust this parameter, you may also wish to increase the lengthwise resolution to at least 6. Note that this parameter does not affect beta splines.

• Set Width to Property: This option is used with the ``Variable Width'' type of worm. Spock displays a pop-up menu to ask which property the user wishes to be represented as the worm's width. The maximum value of this property is set to twice the worm width parameter, and the minimum value is set to 10% of the width parameter. All other values are linearly interpolated between the two extrema.  
• Use Worm Shadows: This option toggles the use of a different color for the narrow edges of rectangular and secondary structure worms. The details of the worm shadow color are explained in §5.2.1.
• Rectangular helices: This toggle controls the cross section of helices in a secondary structure worm. If it's off (default) the cross section is an oval. Turn this on to get rectangular helix cross sections.
• Rectangluar DNA/RNA: This toggle controls the appearance of nucleic acid backbone representations. When on, all nucleic acids are drawn with a rectangular backbone. When off, the style for these backbone representations is the same as the primary worm style.
• Beta spline: This option uses a beta spline for the basis of the worm. Beta splines are smooth, but do not necessarily pass through all the CA coordinates.
• Cardinal spline: This option will use a cardinal spline instead for the worm basis. Cardinal splines may not look as smooth as a beta spline, but the spline will pass through all the CA positions. The appearance of the cardinal splines may also be affected by the tightness factor found in the ``Edit worm parameters'' menu option above. Note that in secondary structure drawing mode, strands may not pass through the CA positions because of strand smoothing. If you wish, you may set the strand smoothing steps to 0 in the ``Edit worm parameters'' dialog. A cardinal spline with strand smoothing set to 0 will insure that the worm passes through all CA's.
• Solid: This option is the default which is a worm consisting of filled polygons.
• Mesh: This option causes spock to draw the worm as a wire frame model. Note that worm segments with a ``negative'' color are always displayed as wire-frame meshes § 5.2.1.
• Edit Worm Material: A short cut to the worm material editor. See §6.11.4.

   

CA trace

  This menu controls the display of CA trace backbone representation. CA traces all have the same color, unless the cac=n command has been issued, which colors CA traces sequentially or the cac=b[ond] or cac=a[tom] commands have been issued, which colors the CA trace according to the bond or atom color properties, respectively. The menu options are as follows:

• Cylinder: Display as cylinders.
• Line: Display as lines.
• Line width: Set the width for the line display mode. The cylinder display mode uses the bond width parameter as the width.
• Edit CA Trace Material: A short cut to the CA trace material editor. See § 6.11.4.

   

Surfaces

  This menu is the main interface to the surfacing routines. Spock can create and display both molecular and accessible surfaces for molecules. Note that unlike worms, there is no default definition for surfaces, so surfaces must be defined before they can be displayed.

 
• Build Molecular Surface: This option will prompt for a selection string (See §5.3) specifying which atoms are to be included in the surface calculation, and a grid resolution which determines how accurate the surface is. There is no upper limit on the grid resolution, but be prepared to wait if you choose higher than the default 65. The molecular surface is defined as the boundary of the surface you would get if you rolled a water molecule along the atomic surface. The probe water radius may be changed via the ``Probe radius'' option of this menu.  
• Build Accessible Surface: This option also prompts for a selection string, and grid resolution but the accessible surface is built instead. The accessible surface is defined the path traced out by the center of the water molecules described above for the molecular surface, or alternately the outer surface of the included atoms, where each atom's radius is expanded by the radius of a water molecule (1.4 Ångstroms by default). The probe water radius may be changed via the ``Probe radius'' option of this menu.
• Find connectivity: This option can only be used after a surface has been built. It will generate subsets for each independent (non-connected) surface. These subsets will be called either mainN or cavN (where N is an integer) depending on if it's an convex outer surface or a concave inner cavity, respectively. The name, volume, and surface area of each cavity will be written to the textport for each subset. The system macro Color_surface_subsets may be used to color each of the subsets generated from this routine with a different color.  
• Probe Radius: This option prompts for the value to use for the probe water radius for the surfacing routines. There is only one probe radius in spock, although as a convenience, it may be set from several locations, including the Surface Area menu §6.6.3.
• Solid: This option indicates that surfaces are to be drawn with filled polygons, creating a solid appearance.
• Mesh: This option indicates that surfaces should be drawn with a hollow wire-frame representation.    
• Transparent: Draw the surface transparently. The degree of opacity may be changed via the material editor (§ 6.11.4). In my (subjective) opinion, transparent surfaces look better if you turn off the fog material property by setting the Fog start and Fog end parameters to the same value in the material editor.
• Mixed solid/transparent: This mode allows solid and transparent surfaces to be drawn together. Vertices with colors greater than 50 are drawn transparently, while colors 50 and below are opaque. This only applies if ``Nice transparency'' is turned on in the graphics menu §6.11.
• Show top surface only: This option only affects the transparent surfaces when ``Nice transparency'' is turned on in the graphics menu. It toggles between showing only the top surface of a transparent object and showing all layers.
• Reduce when building: This toggles a routine which will eliminate small triangles when building a surface. This is generally not needed for molecular and accessible surfaces, but it improves the appearance of isopotential contours.  
• Cap clipped surfaces: This option determines if surfaces that are clipped via an auxiliary clipping plane (§ 6.11.4) should be capped or not. Having a cap makes the surface appear to be solid instead of hollow, and may help to eliminate unnecessary clutter from an image. The color of this cap may be set via the cc=n command, where n is a color number.  
• Resmooth surface: This option will re-run the surface smoothing algorithm on all currently defined surfaces, which may improve the appearance, but will result in some loss of detail. This loss of detail can actually be quite helpful, as molecular and accessible surfaces are often complicated constructs, and multiple smoothing passes will filter out unnecessary details, leaving the key features intact. This may be used to locate binding pockets in some cases, as demonstrated in the tutorial in §8.11.    
• Swap front/back faces: Normally, surfaces are displayed with the outside colored normally, and the inside colored with the back face color (§6.11.4, 6.11.5). Using this option, you can invert this, so that the inside face is colored. Alternately, you may color both faces with the same color, see §6.11.5.
• Edit Surface Material: A short cut to the surface material editor. See §6.11.4.

 

Constructive Solid Geometry

    Spock now has a simple constructive solid geometry (CSG) feature. CSG is the process by which complex shapes can be made by the union, intersection and subtraction of simpler primitives. This is implemented in spock primarily to facilitate molecular modeling/docking/drug design, etc. with molecular surfaces. The most heavily used mode is expected to be the intersection mode, where only the parts of surfaces that overlap with another surface are drawn. Other modes (difference and union) are also available, but are less useful for molecular modeling. To give a brief example of how CSG could be useful, consider looking at a dimer interface, or the interaction between an enzyme and a postulated substrate analog. Traditional ways to tell if and/or where these surfaces overlap would be looking at distance calculations, or by eyeballing the surfaces. Since the surfaces may be quite complicated, detecting overlap this way is sometimes difficult, and distance calculation results are also complicated to interpret. With constructive solid geometry, you simply build one surface for the enzyme and one for the substrate (or one for each monomer in the dimer). Enter into CSG mode, select surface 1 (s=1) for set A and surface 2 (s=2) for set B, and then select ``A u B'' (A union B) from the CSG menu. The only part of the surface that would then be rendered is the region where the two surfaces overlap. If no surface is drawn, there is no overlap.

The menu options are:

• New sets: Enter new surface subset selections. In the simplest cases the sets are simply s=1 and s=2, for the entire first and second surface, but other surface selections are possible.
• CSG mode: This must be toggled on for the CSG mode to be active. If off, the surfaces are rendered normally.
• A only/B only: Show only the A surface set or the B set, where A and B are the sets defined in the ``New sets'' option.
• A u B: A union B. Show both set A and set B.
• A n B: A intersection B. Show only the parts of A that are also in B.
• A - B: Show the parts of A that are not in B.
• A - B: Show the parts of B that are not in A.

Caveats for using CSG:

• This is a simple-minded implementation of CSG, which doesn't handle surfaces which have multiple concavities along the line of sight very well. There are more robust CSG algorithms available. If you're a programmer and are interested in implementing a more robust algorithm, please get in touch with us.
• The CSG algorithm corrupts the depth buffer. You should only have surfaces turned on in the display menu when using CSG. Otherwise, the surfaces may appear to be on top of objects which they should actually be behind. Again, a more robust CSG algorithm could potentially fix this defect.
• CSG uses the stencil planes, and so do transparent surfaces. Therefore CSG should not be used with transparent surfaces or mesh surfaces. Only solid surfaces are supported in CSG mode.
• Since they both use stencil planes, CSG mode overrides the ``Cap clipped surface'' setting, and disables it.

   

Contours

  Spock can calculate and display two-and three dimensional contour lines and surfaces of electrostatic potential. The menu options are as follows:

• Add 3D Contour: This will prompt for a contour level, which is the threshold value to use for the contouring. It will also prompt for a color number to use for the surface. A 3D surface will be calculated.
• Change 3D Contour Color: This option will pop up a menu of currently defined contours, and allow the user to select one. If a valid contour is selected, the user will also be prompted for a new color to use for the contour. Like all objects in spock, contours given a color of zero will not be displayed.  
• Delete 3D Contour(s): This option will pop-up a menu of the currently defined contours, and allow the user to select one to delete. There's also a ``Delete all'' option. These contours will then be deleted, and their memory reclaimed.    
• Add 2D Contour, Change 2D Contour Color, Delete 2D Contour(s): These options are identical in function to their 3D counterparts. Spock displays 2D contours on a movable plane parallel to the screen. The position of this plane along the screen Z axis (into and out of the screen) may be changed via the Clipping Tool §6.11.4. Unlike their 3D counterparts, 2D contours are calculated interactively, and change as the molecule rotates. Since they're recalculated each time the scene is drawn, they slow performance slightly, but they do not take appreciable memory.    
• Display modes, Solid, Transparent, Mesh: The display modes control the visual appearance of the 3D contours. Solid contours are rendered with filled polygons, transparent contours are stippled, and mesh contours are draw with a wire-frame. The degree of opacity for transparent surfaces may be changed using the material editor, §6.11.4.

  Unlike molecular and accessible surfaces, the solid and transparent modes are not global, but are applied only to an individual contour 1) when a new contour is created, 2) the color of an existing contour is changed or 3) when a contour is smoothed. The mesh mode, however, is applied globally and instantly.

• Edit Contour Material: This option is a shortcut to the material editor §6.11.4.
• Build Consensus Surface Contour: This item is useful for determining the area two accessible surfaces have in common. This option will prompt for two selection strings (set 1 and set 2) and then construct an accessible surface for each selection. Finally, a contour will be constructed around the area the two surfaces have in common. This option does not affect any of the user-defined surfaces, but it does overwrite the charge map, if any.
• Build Difference Surface Contour: This item is similar to the Consensus Contour option, except in this case the final contour shows the areas where two surfaces differ. This is quite useful for homing in on those areas where two similar structures differ.
• Show top surface only: This option only affects the transparent contours when ``Nice transparency'' is turned on in the graphics menu. It toggles between showing only the top surface of a transparent object and showing all layers.
• Reduce when building: This toggles a reduction algorithm that saves memory and improves the appearance of 3D contours. It should normally be left on, but there's a slight speed improvement from toggling it off.
• Smooth contour: This option will apply a nearest-neighbor smoothing algorithm to the contour. Users are prompted for the number of times to apply the smoothing, and then presented with a menu of currently defined contours, from which the desired contour may be chosen. No smoothing of contours is done when they are created. As with molecular and accessible surfaces, a few rounds of smoothing will result in a decrease in the complexity of the contour.

   

Density maps

    Spock can read and write XPLOR-format electron density map files, and display the electron density in several formats. Spock may also be used to perform user-defined calculations on density maps via the command line calculator, or the Properties math menu (§5.5, 6.6.2). Spock has eight slots for electron density maps, called rather imaginatively, Map 1 through Map 8. Spock can also display up to eight contours of any of the 8 maps (more, actually with the 3D contour object option discussed below). The maps need not come from the same file or have the same dimensions, or even be for the same protein--they are totally independent. For each of the eight contours you must specify which of the eight maps is to be contoured--contour 1 can be any map, not just map 1. Spock also supports the notion of a current map. Read and write operations apply to the current map only, and the current map is the default when an new contour is created. To read in a second map into the Map 2 slot, the current map needs to be set to Map 2 with this menu, and then the file may be read via the read= command or via the menus.

Density Contours 1-8

These menu options toggle the display of the contours. When turning on a contour the user is asked to set or verify the contour's parameters. The parameters are:

• Which map: This should be 1 or 2, depending on which map you wish to contour. The default is the current map, or the previous map for the contour.
• Contour level: Where the map should be contoured, usually 1.0 for XPLOR maps.
• Color: The color to use for this contour, blue (4) is the default.
• Center on atoms / X, Y, Z: If the default of none is overridden, the contour will be build centered on the atoms specified for this option. You may wish to enter all for this filed to center on the entire structure. If the center on atoms field is left as none, the contour will be centered on the XYZ vector provided (in orthogonal Ångstrom coordinates). The default XYZ coordinates are the coordinates of the last picked atom, unless the last picked object wasn't an atom, in which case the XYZ coordinates of the center of rotation are used instead. This is designed to make it easy to manipulate density contours if you've torn off the Alter density menu. Simply pick an atom, and toggle the density contour on and off, and the new contour will be centered over the atom you picked. Finally, you may wish to enter picked here, and the map will be centered on the last picked atom. See the Tutorial 8.8 for a great use for this.
• Length: The length of a side of the contour, in Ångstroms.

Update maps

This option will cause the displayed contours to re-created. If the contents of the underlying maps have changed (by reading a new map, doing a calculation), this can redraw the contours based on the new maps.

Make 3D contour object

    This will create a 3D contour of the electron density map with the specified options, using the same algorithm (marching cubes) used for the ``3D contours'' menu options, which is generally applied to the electrostatic potential maps. After this contour is created, it is under the control of the Alter contours menu, §6.4.6. Users may want to create this type of contour if (heaven forbid!) they want to show more than eight maps at a time. A much cooler use of this is to create the contour and then make it transparent with the Alter contours menu. Be the envy of other crystallographers! Show your density maps as translucent solids! For an even cooler look, go back and contour with the same parameters as a normal electron density map overlaid on the translucent solid.

Current map

This sets the current map for read/write operations to the specified slot.

Delete map

  Density maps may take large amounts of memory. In order to free this memory for other uses, you may wish to explicitly delete the map. You do not need to retain a copy of the map after it has been contoured, unless you wish to re-contour it at a different time.

Delete all maps

This option will delete all 8 maps.

Clone map

This option will copy the current map into the specified slot number.

Make positive/negative mask

    Spock can create density mask maps from atomic data. These maps are binary in nature, in that they have density values of 1 or 0. A positive mask has a density of 1 within the Van der Waal's radius of an atom (plus an offset), and 0 elsewhere. Negative masks are the reverse--0 within atoms, and 1 elsewhere. Density masks may be used for a variety of purposes. Some simple examples are to use masks to clean up a real electron density map for presentation purposes, to show where atoms may be missing in a model, and to create/manipulate masks for solvent flattening when attempting to solve a crystal structure.

If a real electron density map has already been read in, the created mask has the same dimensions and parameters as the real map, otherwise, a new map is allocated with dimensions that will just cover the currently defined atoms. Newly allocated maps are created in orthogonal Ångstrom coordinates. In either case, spock prompts for the radius expansion factor, which is the value to be added to the Van der Waal's radius of each atom. For instance, if you want a mask of the space that's within 5 Ångstroms of an atom, enter 5.0 here. The mask is created and stored in the next slot number (1-8) after the current map. If this would overwrite an existing map, you're asked to verify the operation.

Make positive binary map

This option converts the current map containing continuous density values to a discrete binary representation, where density greater than the specified threshold is mapped to 1, and density less than the threshold is mapped to 0. The new map is created in the next slot number. For example, if the current map is map 1, the new map will be created in slot two.

Make negative binary map

This option converts a map containing continuous density values to a discrete binary representation, where density greater than the specified threshold is mapped to 0, and density less than the threshold is mapped to 1. The new map is created in the next slot number. For example, if the current map is map 1, the new map will be created in slot two.

Make pseudo density map

  Spock can also create a pseudo-density map. These maps are generated from atomic data and have electron density centered in a Gaussian distribution about atomic centers, such that the density at a distance of 1 atomic radius is 1.0. In many respects, these pseudo-density maps work like the masks just described, in that if there's an existing density map defined, the new map will have the same dimensions, otherwise a new one that covers the atoms is created in orthogonal Ångstrom space.

Orthogonalize map

This option will orthogonalize the current map, creating a new map with 90 degree angles and 1 Å grid spacing in the next slot.

Wide lines

This toggles between single and double width lines in density maps.    

Helices

    Spock can calculate the axis of any helices in the protein or DNA molecule loaded, and display the axis in the graphics window as a cylinder. The helix definitions are taken from 1) the PDB file's HELIX records, if present 2) from a DSSP file, see §6.1.1 or 3) secondary structure assignments made via the set structure command or the secondary structure editor (§6.7.6). (Helix definitions for nucleic acids must be via the third method, as they are not included in HELIX records of PDB files, and DSSP will not assign nucleic acids.) Spock uses any of 5 different methods to find the helical axis. These methods are all explained in detail in reference [3]. After the axes are calculated, summary information for each helix is written to the textport, including: the axis vector, the initial point, and the final point of the displayed axis.

 
• Build: This option tells spock to calculate the helical axis for the currently defined set of helices. This option must be selected before any helices will be displayed.
• Kahn method: This option tells spock to fit helices with the Kahn algorithm [6]. Briefly, in this method, points which lie on the axis are found by vector algebra. The angle between three consecutive (evenly-spaced) atoms is bisected, resulting in a vector , that points towards and is perpendicular to the helix axis. Repetition of this process with a different set of atoms gives a second perpendicular to the helix axis (). As and are both perpendicular to the helix axis, the cross product gives the direction vector of the axis, this process is repeated for all sets of three CA's in the helix and the results averaged.
• Åqvist method: Åqvist's method [1] fits the atom coordinates to a cylinder by minimizing the root mean square deviation of the distance from each atom to the axis, where the distance to the axis is a function of 6 variables, 3 for the position vector and 3 for the direction vector. This method requires a minimum of 5 residues for protein helices and 12 residues for DNA helices.   
• Rotfit method: This method [3] maps the helix (H) to an identical copy of itself (H'), but one atom out of register, so that atom i+1 of the first helix is mapped to atom i of the second helix. These two helices are then superimposed by the method of quaternions [8]. The axis of rotation necessary to superimpose H and H' is the helix axis.
• Parlsq method: This is the ``Parametric Least Squares'' method [3]. If the atoms in a helix are numbered sequentially (call the sequence number t), starting with zero for the first atom, three-dimensional linear least-squares fitting can be accomplished by taking advantage of t in order to parameterize the line containing the axis vector, if the atoms are evenly-spaced along the helix direction vector. In general, any line in three-dimensional Cartesian space may be represented by the equation: where is the vector representing the line, and are the position and direction vectors, respectively, and t is the parameter. The vectors in this form of the equation may be decomposed into their component vectors, essentially projecting the line onto the tx, ty, and tz planes. The equations are:
  
  Each equation is now in the standard form for a line in two dimensions (r = p + td), and the three lines can be fit individually by a standard least-squares procedure. The helix axis is then .
• Eigenfit method: This method finds the helical axis by the Eigenvector method. After the data set is translated so that the center-of-mass is at the origin (O), a least-squares matrix M is constructed such that:
  
  where ) are the coordinates of atom i. The eigenvector of this matrix with the highest eigenvalue is an approximation of the helical direction vector . Note that unlike the parlsq method, eigenfit does not require the data to be evenly spaced along the direction vector. Both the parlsq and eigenfit methods simply find the best-fit line through the data, as opposed to finding the true helix axis. This line better approximates the helix axis as the length of the helix increases. At shorter helix lengths, the accuracy of the approximation depends on the number of turns; helices with non-integral numbers of turns may skew the results. This effect is attenuated with longer helices.
• Circular positioning: Each of the methods spock uses to determine the helical axis also determines the position vectors used to display the axis on screen. However, for some methods the axis may not lie in the center of the helix. The circular positioning implements an additional fit, where the atoms in the helix are projected onto a plane perpendicular to the axis. The center of the best-fit circle through these points is then used to re-calculate the position vectors.
• Rounded cylinder ends: This option toggles round vs. flat ends for the helix cylinders.
• Alter radius: This option prompts for the radius to use for the cylinder representations of the axis. Unlike the Control Panel (§6.1.8), there is no maximum radius here. Caveat ussor.  
• Secondary structure editor: This option, described in §6.7.6, allows interactive re-definition of the helices.
• Edit Helix Material: A short cut to the Helix material editor. See §6.11.4.

   

Sheets

  Spock can also calculate the axis of individual strands of Beta sheets, by the same methods as for helices (§6.4.8). Since strands are highly non-linear, these results are often not as good as those produced for helices. Often, ``Parlsq'' or ``Eigenfit'' produce better results for sheets. All of the menu options are the same as described above for helices.    

DNA spokes

  This menu controls the options for the DNA ``spokes'' representation of base pairs. The ``Edit color assignment'' option puts up a menu where you may choose which colors are used for each type of base representation. The ``Edit DNA material'' option is a shortcut to the Material properties editor, see §6.11.4.    

Labels

    This menu controls the appearance of atom labels and annotations. A ``label'' refers to a string of characters attached to an atom that rotate with the molecule. An ``annotation'' is a text string that is independently positioned on the screen and does not rotate when the molecule is rotated. Annotations are positioned via the mouse in the ``Move Annotation'' mode (§6.9.3). There are two types of labels for atoms, ``Standard'' and ``Custom''. Each atom can have either a standard or a custom label. A standard label is derived from the atom's name and residue in some pre-determined way. A custom label is entered by the user, and may or may not contain the same information as a standard label would. All custom labels will be in a single font and all standard labels will be in a single font, which need not be the same as the font for the custom labels. However, each annotation may be in a different font. See §6.9.3 for information on editing labels to create custom labels.    

• Custom: Pops up a font selection box for the custom labels. The font selection box consists of a scrollable list of the available fonts (which will be system-dependent), a slider to set the size, a sample window, and two buttons ``Apply'' and ``Dismiss''. Fonts are selected from the list and may be sized via the slider. The sample window will display a label in the current font and size. The font information is not passed back to the main window until and unless ``Apply'' is selected. Pressing ``Dismiss'' removes the font selection box.
• Standard: Selects the font for the Standard labels as above.  
• Annotation:Selects the font for the current annotation as above. This font will apply to any newly created annotations. If there is a current annotation highlighted (via the ``Edit label/annotation'' or ``Move annotation'' options of the Picking menu §6.9), the font will also apply to the highlighted annotation. In this manner it's possible for different annotations to be in different fonts. Note, however, that it's fairly expensive to change fonts, (or even sizes) and that it's best to keep the total number of fonts low. If possible order your annotations so that those that are in the same font are together, to keep from having to switch back to a font that you've already used.
• Scale labels: If checked, this option causes spock to scale the labels with the rest of the molecule. Otherwise, labels remain a constant size when the molecule is scaled.
• Add annotation: This option prompts for an annotation string to be added to the image. Initially, annotations are placed near the top center of the view, but annotations can be moved via the ``Move Annotation'' feature of the Mouse menu (§ 6.9.3).
• Chain Name, Residue Name, Residue Number and Atom Name: These options are toggles for what components of an atoms identity are part of the standard label string.
• Standard Label Format: These options indicate in what order the standard label components are displayed. Of course, items not selected for the standard label are skipped. At present, these are the only standard formats available.
• Standard label offset: This option prompts for an integer to use as the label offset, which is simply the number of spaces that should come before standard labels. This will have the effect of moving the standard labels to the right. There is no way to move standard labels to the left. If you need to do this, you'll have to use an annotation instead.

     

Interactions

  An ``interaction'' is simply a relationship between two atoms with an associated strength or magnitude. Spock has two types of interactions, ``distance'' and ``intensity'' interactions. A distance interaction, as the name implies, is simply the distance between two atoms. Distance interactions are usually displayed by a dotted line, or a series or spheres between the atoms in question with a label indicating the distance. Intensity interactions, on the other hand, require some external value for the strength of the interaction. Intensity interactions are generally displayed as cylinders, where the radius of the cylinder is proportional to the strength of the interaction, and they usually do not have labels. Salt bridges specified by CONECT records in PDB files are treated as interactions with an intensity of 1.0. Interactions may also be created interactively via the Picking menu § 6.9, or they may be read from an external file § 6.1.1. The menu options are as follows:

 
• Distance Interaction, Intensity Interaction: These two items are alternate choices for the current interaction type. Newly created interactions will be drawn in the indicated type. Also, if the picking mode is set to ``Set interaction style'', the selected interactions will be changed to this type.
• Dotted Line, Solid Line, Cylinder, Rounded cylinder Spheres: These options set the current display style for interactions. The current interaction style is applied as above for the interaction type.  
• Show Label: This toggle sets the label flag for the current interaction style. Only if the toggle is set will a label be drawn. Setting the interaction type to ``Distance'' turns this on, and ``Intensity'' interactions turn it back off. After the interaction type has been set, users can override the label setting by using this toggle. The font for this label is the same as the standard label font (§6.4.11).  
• Delete all interactions: This option will clear the internal interaction table, deleting all interactions.
• Set style for all interactions: This entry will set all currently defined interactions to the current interaction style (cylinders, lines, etc.).
• Set maximum interaction radius: This option sets the radius to be used for the interaction with the highest intensity. This parameter may also be controlled by a the control panel (§ 6.1.8).
• Copy HBonds into interactions: This option will create a distance interaction for each H-Bond in the selected set of atoms. The intended use of this is for these interactions to then be saved as AMBER constraints (§6.7.9).
• Edit Interaction Material: This is a shortcut to the Material Editor §6.11.4.

    Interactions have a few properties that are not set by the menu options. The first property is the concept of an ``interaction type'' which is simply an integer from 1-255 that users may use to categorize different interactions. The primary purpose of the interaction type is to support MORASS files, which specify this quantity, but the type may also be used do divide interactions into groups, say hydrogen bonds and salt bridges, etc. The interaction type is set by the command set it=n, where n is the type number. This command may be limited by a selection string, (e.g. set it=4,rn=32 or set it=2,in=5).

The interaction strength or intensity value may be set via the command set iv=X where X is any real number. This command may also be limited by a selection string, of course. Like all other objects, the interaction color may by set by the command ic=N, where N is a color.

A list of the current interactions is given by the ilist command, which, again, may be limited by a selection string.

Finally, there is a unique selection string for interactions, the ``rank'' interaction. It's possible to limit selections so that they apply only to the strongest (most positive) or weakest (most negative) interaction for a particular atom. Since an atom may contain several interactions which may clutter the display, this selection is provided to make it easier to select only the most extreme interactions. The syntax for the selection is ip=1 for the strongest interactions and ip=-1 for the weakest interactions. For example, ic=$blue,ip=1 will color the strongest interaction from each atom blue. Note that this syntax, although borrowed from GRASP [11] does not have exactly the same effect as the GRASP command, as other possibilities allowed in GRASP such as ip=2 are not implemented. The incremental advantage of such commands is small, and not worth the effort it would take to code them given the data structures spock currently uses.

To recap, the available interaction commands are ic, set iv, set it, and ilist to set the interaction color, value, and type and to list interactions, respectively. The selection strings applicable to interactions are ic, iv, it, and ip to limit based on color, value, type, and rank, respectively. Atom selections may also be applied to interactions.    

Spectra

  Spectra are described in §6.3.19. These menu items control the format and properties of the spectra. Since the options are identical for worms and surfaces, they will be described in general terms below.

• Set spectrum property: This option displays a submenu with which you can select which atom or vertex property is represented by the spectrum. For instance, you can choose to have worms colored by atom property 2 (b-factor), or surfaces colored by distance.
• Color with spectrum: Surfaces or worms are not colored according to the spectrum parameters unless this option is on. When off, surfaces and worms are colored according to their assigned colors.
• Show spectrum scale: This option determines if the text part of the spectrum object is displayed.
• Vertical spectrum: This controls the orientation of the spectrum object, if vertical is off, the spectrum is oriented horizontally.
• Edit spectrum: This option displays a dialog box allowing users to edit all the spectrum properties, many of which may also be set with the mouse as described in §6.3.19. The parameters are:
  • Minimum, Median, and Maximum value: these values are the extrema and the internal value that are used to control the color interpolation. They need not correspond to the true extrema (or midpoint) of the property under consideration. By default these are assigned to as the mean value of the current property, and the mean plus or minus one standard deviation.
  • Minimum, Median, and Maximum color: These are the colors that are used for the interpolation. Values at or below the minimum value as defined above will be displayed with the minimum color, similarly, values at or above the maximum value will be displayed with the maximum color. Intermediate values will have their colors linearly interpolated. The color numbers correspond to the colors in the color palette, accessible via the ``Graphics Color tool'' menu.
  • Scale color: The color number used to draw the text scale.
  • Scale divisions: The number of divisions on the scale. This affects only the display of the spectrum object, not the color interpolation.
  • Scale pointsize: The size of the text for the scale.
  • Scale precision: The number of decimal points in the displayed scale. Does not affect color interpolation.
  • Magnification: The size of the spectrum on the screen. The units are the same as for the global zoom factor. The default is 0.5.
  • X, Y: The fractional screen coordinates of the center of the spectrum object. Fractional screen coordinates range from 0 to 1 with the origin at the lower left corner.