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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).    

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).

   

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.

   

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:

   

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.

 

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:

Caveats for using CSG:

   

Contours

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

   

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:

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.

   

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.          

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:

    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.

 
next up gif contents index
Next: View Up: Menus Previous: Display

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999