Modeling

  This menu provides an interface to spock's modeling features. There will be more features added in the future, but the currently implemented features are described below.  

Sort atoms

  This command resorts atoms in each residue to the standard order required by the PDB. This should be unnecessary for files downloaded from Brookhaven. However, many software packages produce non-standard PDB files with the atoms not in the proper order. This makes it difficult to compare two structures from different programs on an atom-by-atom basis, and causes other problems. Re-sorting pdb files with this command should fix these problems. This sorting depends on the file $SP_AALIB/atom.lib, so changing $SP_AALIB can be used to use a different sorting order.  

Superimpose

    Implements a superimposition algorithm based on Mackay's quaternion method [8] (as described for helices in §6.4.8). When superimpose is chosen, spock displays a dialog box with four input fields. The first two are prompts for two selection strings (§5.3) that describe the atoms to be superimposed. There should be the same number of atoms in each selection. The third selection string specifies to which atoms the superposition should be applied. This selection string may be different from either the first or second selections above. Most commonly, the original sets will be alpha carbon atoms, and new sets would be all atoms in one molecule or another. The final option for this dialog specifies the direction for the superposition matrix to be applied. This may be either ``First -> second'' or ``Second -> first'' depending on the direction you wish the final set of atoms to move. After you press Ok in this dialog, spock will calculate the optimal superposition matrix, and then transform the atoms selected in the third set according to that matrix.  

Undo superimpose

Obviously, this command reverses the last superposition. Re-application application of this undo will redo the superposition again.  

Delete Atoms

    This sub-menu has several options for deleting atoms from spock's memory, ``Molecule'', ``Selection'', or ``All''. ``All'' deletes all atoms (after prompting for conformation). This option clears all internal variables as well, returning spock as nearly as possible to the initial state, this is the same as the ``FileDelete All'' menu option (§ 6.1.3. ``Selection'' prompts for a selection string (§ 5.3) of atoms to delete. (This is the same as the delete command.) ``Molecule'' constructs a pop-menu from the currently defined molecules from which the molecule to be deleted may be selected. To delete a molecule from a History or Command file (§7), choosing ``Selection'' and then entering the molecule number is probably a better option, because of the fact that the ``Molecule'' option's pop-up menu includes structure-specific information that may vary from one file to the next.  

Copy Atoms

  This submenu has the same options as the Delete Atoms menu, but instead of deleting the atoms, they are copied into a new molecule. All atom properties are copied as well, except that if there are any surfaces defined, the new atoms do not ``own'' any surface vertices. The new molecule number is printed out, and can be checked later via the mlist command. This option is most useful when used with the subset menu options which allow you to move defined subsets independently, see § 6.8.  

Secondary structure editor

  This option pops up the secondary structure editing dialog, inspired by a similar facility in SETOR [4]. Users can use this dialog as a more convenient interface to setting the secondary structure than the command-line set structure command, but both have the same effect.

A linear cartoon representation of the secondary structure of a single molecule is displayed. The cartoon of secondary structure uses red ``squiggles'' for -helices, large blue boxes with arrow heads for sheets (this in mnemonic Blue and Beta), magenta boxes for turns, and yellow lines for coils. Moving the mouse over a symbol will update the status line with the identity of the residue under the cursor. Pressing the mouse button over an a symbol will change the structure for that residue to the current structure type (helix, sheet, coil, or turn) as indicated by the ``Mode'' section of the status line. The current mode may be changed via the Options menu of the dialog. The Options menu also allows users to set which molecule to display.

There are three buttons in the dialog, ``Apply'', ``Revert'' and ``Dismiss''. The secondary structure dialog edits a copy of the secondary structure information, not the information itself. Therefore, changes are not active in the main window until ``Apply'' is pressed, which updates the main display with the newly-defined secondary structure information. This can be seen visually if the current molecule is displayed with a secondary structure ribbon (§6.4.3). It's important to note that changes are made for all molecules, not just the one currently displayed in the editor, so you don't have to apply the changes before changing displayed molecules. The ``Revert'' undoes any changes you've made since the last apply (again, to all molecules, not just the currently visible one). Finally ``Dismiss'' hides the editor, and cancels any changes you've made.

The secondary structure also interacts with the command-line set structure command. Using this command while the secondary structure editor is visible will overwrite any changes you've made in the editor, but not yet applied. Similarly, altering the secondary structure information in any other manner (e.g. running or reading a DSSP file § 6.1.1 and 6.7.8, or a new PDB file) will also overwrite the information in the editor.

Altering the secondary structure definitions also causes spock to recalculate the table of defined helices and sheets used for the Display Helices and Display Sheets menu items or as printed out by the hlist and slist commands.

The secondary structure editor may also be used to assign helical structure to nucleic acids. Helical regions defined in this manner will have an axis cylinder displayed if the Display Helices menu option is on. These helices will also show up in the helix list via the hlist or show helices commands. For visualization purposes, probably only one strand of a double-stranded helix should be assigned to helical structure, as the two strands will have a slightly different axis. Note that it is possible to assign other structure types (sheet or turn) to nucleic acids, but those assignments are meaningless.    

Calculate Secondary Structure

    Calculates the secondary structure from hydrogen bonding parameters via an internal implementation of a DSSP-type algorithm [5]. For each residue, this routine prints the summary structure assignment (helix, sheet, turn or coil) as well as any n-turns, n-helices (n=3,4,5) or sheets the residue participates in. This routine sets the ``structure'' property (§5.2.4.)  

Run DSSP

  Runs an external DSSP program on all currently defined atoms and extracts secondary structure information from it. For more information see § 6.1.1. This routine sets the ``structure'' property (§ 5.2.4.)  

Amber interface

Sorry, this feature is not yet documented.  

Hydrogen bonding

Spock can perform calculations to determine the probable location of hydrogen bonds. Although not perfect, these calculations may prove useful. Once calculated, the position of the bonds may be displayed with the ``Display->H-Bonds'' menu option. There are several options controling spock's H-Bond calculations.

• Simple, DSSP, HBPLUS: These three items select the rules which spock uses to calculate H-Bond positions. The ``Simple'' rules use a set of empirical distance and angle constraints which are fairly accurate, and capable of finding most H-Bonds. The ``DSSP'' rules use an energy function but will only find backbone hydrogen bonds. Finally, the HBPLUS rules use a more complex set of distance and angle constraints than the Simple rules, but require the position of the Hydrogen atoms to be modeled, which is currently only done for the backbone. The only option which currently finds side-chain atoms is the ``Simple'' rule set.
• Find H-Bonds: This option actually runs the calculation and creates the H-Bonds.
• Fixup H-Bonds: The H-Bond calculation above finds bonds to and from heavy atoms, ignoring any explicit hydrogens. If there are explicit hydrogens in your structure, this option will ``move'' any defined H-Bonds to the closest explicit hydrogen.
• Delete all H-bonds: This option deletes all the H-Bonds from memory. You may wish to do this before changing the rule set (Simple,DSSP,HBPLUS) and re-calculating the bonds.
• Edit simple H-bond constraints: This option allows users to change the criteria used by the Simple rule set. You are prompted for the maximum distance between the two heavy atoms, and then for three angles (DAX, and the XDA Maximum and XDA Minumum). DAX is the angle between the donor and acceptor heavy atoms, and another heavy atom bonded to the donor. Only regions with angles greater than this threshold will be considered bonded. XDA is the angle between some heavy atom connected to the donor heavy atom, the donor heavy atom, and the acceptor heavy atom. This angle must be between the max and min values specified to be considered for a H-Bond.
• Print H-Bonding definitions: In addition to meeting the distance and angle criteria above, atoms must be recognized as a donor or acceptor before a H-Bond will be found. This option prints out spock's table of donors and acceptors for your inspection.
• Edit H-Bonding definitions: This option allows you to edit the list of donors and acceptors for a residue type. Users are first prompted for the residue name. If the residue is in the internal table, all atoms in the residue are listed and then the donor and acceptor lists are available for editing. Remember that atom names have exactly 4 characters, so be sure to use exactly 4 spaces for each atom name with no extra spaces. If the residue is not in the internal table, you may define a ``custom'' residue; users may enter the donor and acceptor atoms for these residues as well. NOTE: If a residue is not found in spock's internal list or the custom list, any N is considered a donor and any O is considered an acceptor.

Delete All H-Bonds

    Deletes all currently-defined hydrogen bonds.

Matrix/symmetry operations

This submenu provides several symmetry options, including the ability to apply symmetry operations, and display all symmetry-related molecules.  

Fractionalize coordinates

  If the crystal parameters are set (via the PDB file or the Edit crystal parameters option of this menu) this option prompt for a selection string and apply the crystal scaling matrix to the selected atoms. The atoms coordinates will then be in fractional coordinates. The results of displaying objects while in fractional coordinates are undefined, but things will probably look really funky. Certain symmetry transformations operate on fractional coordinates, so a common sequence would be 1) Fractionalize coordinates 2) Apply 4x4 matrix 3) Unfractionalize coordinates.  

Unfractionalize coordinates

If the crystal parameters are set this option prompt for a selection string and apply the inverse of the crystal scaling matrix to the selected atoms, returning fractionalized atoms back to orthogonal Ångstrom coordinates. Use this option with caution, as it is possible to apply the unfractionalization matrix to atoms which are not in fractional coordinates. If this happens, applying the Fractionalize coordinates option to the affected atoms should restore things to normal.  

Edit crystal parameters

    This option puts up a dialog box that prompts for the current crystal parameters: a, b, c, alpha, beta, gamma and the current space group. To eliminate ambiguity, the full international Hermann-Mauguin symbol should be used, e.g., P 1 21 1 instead of P 21. However spock will recognize most of the common abbreviated space group symbols. Entering the crystal parameters causes spock to re-calculate the scaling matrix necessary for fractionalizing coordinates, and updates the unit cell display.   Spock has a symmetry library file $SP_SYMMETRY_LIB, which it reads to determine which operations to perform for each space group. For structures with non-standard space groups you may need to edit this file and add your space group. The default symmetry library file is in $SPOCK/lib/symmetry.lib.  

Apply 4x4 matrix

  This submenu has the same options as the Copy and Delete Atoms options. After specifying an atom selection, the user is prompted for a 4x4 transformation matrix to apply to the selected atoms. See Appendix E for details on how to specify a transformation matrix.  

Display symmetry

    These options control the display of symmetry-related molecules. ``Unique'' indicates that only a single unit cell's worth of molecules should be shown. ``Full'' indicates that any molecule having any atom in the cell should be shown, and ``None'', of course, turns off the symmetry display. Note that symmetry-related molecules displayed in this manner are simply ``ghosts'' created by applying the appropriate symmetry operators to the displayed image. They are not ``real'' in the sense that they are not copied into memory, and as such have all the same properties as the parent molecule. You can make ``real'' molecules out of the symmetry replicates by choosing the ``Realize symmetry molecules'' option of this menu.

Color by number

  The color by number toggle of this menu is an aid to visualizing the replicate molecules. Choosing this option will cause the replicates to be displayed in a color according to their replicate number (i.e. the parent molecule gets its normal colors, the first replicate gets color 2, the second replicate gets color 3, and so on). This color scheme only applies to objects that are lit by the graphics commands (solid bonds, worms, solid CA traces, surfaces, etc.). Line-based graphics (such as line bonds, hbonds, line interactions) retain the same coloring as the parent molecule. It is not possible to specify different line-drawing colors for the different replicates without actually creating copies of the molecules via the Make symmetry molecules option, at which time they become ``real'' molecules and as such all operations are available for them.

Realize symmetry molecules

As described above, molecules displayed with the ``Display symmetry'' options are not real molecules, but simply replicates of the original image. If you wish to create a symmetry related molecule, you must use the this ``Realize'' option. This will allocate space for a new molecule, prompt for an atom selection, and copy the selected atoms into the new molecule. At this point the new molecule may be treated like any other molecule in spock, including such things as coloring it independently.  

Rotamer control

  This menu is a control panel for rotamer mode which is entered by picking an atom when the Structure editing mode (§ 6.7.13) is set to ``Rotamer''. The entries are:

• Next Display the next rotamer from the list.
• Previous Display the previous rotamer from the list.
• Apply Accept the current rotamer and leave rotamer mode.
• Cancel Revert to the previous coordinates (the coordinates which were current before entering rotamer mode). This is also available the Undo option of the Edit menu.

Note that like TOR and FBRT (§6.7.13), the coordinates are updated immediately when a rotamer is displayed, so that if write out a PDB file before you ``Apply'' a rotamer the coordinates of the rotamer will be in the output file. If you wish to revert the the previous coordinates, you should use the cancel option.

Spock's rotamer library lives in the text file $SPOCK/lib/rotamer.lib. Currently this file is created by running the script dunbrack.sh on Roland Dunbrack's rotamer library from http://www.cmpharm.ucsf.edu/ dunbrack, which is also included in the spock distribution for reference. Users may substitute their own favorite rotamer library for spock's provided they follow the spock format: six space or tab delimited text columns. Column 1 is the three-letter amino acid code. Column 2 is the frequency of the rotamer, and the remaining 4 columns are for for the chi1-chi4 angles, with 0.0 for undefined angles. The data should be sorted such that the most common rotamer is listed first, and all rotamers for a given amino acid should be together. (This text is intentionally repeated in the appendix on file formats).  

Structure Editing

These options allow for the creation and deletion of bonds, a simple mutation procedure, altering torsion angles, and a one-step ability to rotate all atoms bonded to a given atom independently. To use these, select the desired option, and then pick atoms by clicking on them with the left mouse button (button 1). These options will not be active unless the picking mode is set to ``Modeling'' via the Picking menu. Selecting one of these options will set the Picking menu to ``Modeling'', but choosing any other Picking mode will inactivate the modeling functions until the pick mode is again set to modeling.

 
• Make Bond Creates a bond between two successively picked atoms.  
• Break Bond Deletes the bond between two successively picked atoms if it exists.  
• Make H-Bond Creates a hydrogen bond between two successively picked atoms.  
• Break H-Bond Deletes the hydrogen bond between two successively picked atoms if it exists.  
• Mutate Sets picking to mutate mode. See § 6.7.14.    
• TOR This option (named after the FRODO command) allows rotation about a single bond. Selecting this option and then picking two bonded atoms will initiate the TOR movement mode, where mouse movements when button 1 (the left button) are held down are tied to rotation around the indicated bond, instead of global rotations. To end this movement mode, either 1) turn modeling off in this menu, or 2) change the ``Attach motion'' setting of the Subsets menu §6.8. If you have a dial box, the dials will still control the world rotations, unless you've reassigned the bindings (§6.11.5). As described above, there is an undo for this motion, which will revert to the initial state of rotation, or the last lock point. Note that the coordinates of the atoms are updated immediately, so that if a PDB file is written out, the coordinates will reflect the current rotation. It is not necessary to lock a rotation for this to take effect. Also, for efficiency, not all objects are re-built updated with every redraw. Bonds and circle mode atoms will always reflect the current coordinates, but other objects may need to be updated. To update the other objects, toggle them off and on again in the display menu.  
• Rotamer This option enables the use of a rotamer library for finding favored conformations of side chains. Picking an atom when in this mode rotates the side chain for the residue containing the picked atom to the most common rotamer for that residue as specified in $SPOCK/lib/rotamer.lib. You may then use the rotamer control menu §6.7.12 to choose other rotamers, accept a given rotamer, or revert to the previous state.
• TEXTAL This item is currently for internal use. It may safely be ignored.    
• FBRT This option is also named after a FRODO command. FBRT stands for ``Foreground Background Rotate Translate'', or ``Fragment Break Rotate Translate'' depending on to whom you talk. In any case, FBRT allows for the independent manipulation of a group of bonded atoms. The next atom you pick after entering FBRT mode becomes the center of rotation, and all atoms bonded to that atom are rotated/translated about the picked atom. The comments from TOR above about attachment of the mouse apply equally to the FBRT atoms. You may wish to break bonds first to isolate the section you wish to FBRT using the ``Break Bond'' menu option above. Note that FBRT is very similar to the independent subset rotations described in §6.8, but the rotated atoms do not have to belong to a pre-defined names subset. One other difference is that in the FBRT rotations, the origin of rotation is the atom that was picked, whereas in subset rotations, the origin is (by default) the same as the world center of rotation.
• Modeling off Turns off modeling mutate mode and sets the pick mode to ``Identify'' (See §6.9.)

 

Mutate to

This sub-menu allows the user specify a residue type for spock's rudimentary mutation scheme. When in mutate mode, picking (clicking on an atom or bond §6.9) any atom will cause that residue to be replaced by the currently defined residue. Currently, this is an extremely simple procedure that only effects the side chain of the residue, and does not perform any sort of energy minimization or steric collision checking. This will be addressed in a future version.

NOTE: Non-standard PDB files may not have their atoms in the order specified by the PDB. For example, XPLOR produces PDB files with the C and O atoms after the side chain, and may produce nucleic structures which do not have all the sugar and phosphate atoms listed in a residue before the base atoms. These non-standard PDB files should be fixed before attempting to perform mutation on them.     Mutation is performed by reading the new amino acid type from the amino acid library, (in the $SP_AALIB directory), and superimposing the CA-CB bond between the current and new residue. For mutations to glycine, the side chain is simply dropped. For mutations from glycine, the position that the CB should occupy is calculated from the rest of the backbone geometry. Note that when mutating to a proline residue, the name of the new residue MUST be PRO. The mutation algorithm has to handle proline residues slightly differently from the other residues and needs this clue to tell it what to do. The proline in the default library has this name, so this should not be a problem, unless you've modified the default library.

Mutate also expects the atom names to be in accordance with PDB specifications, particularly with respect to DNA and RNA. The atom names mutate expects are: (4 characters each, _ for blank)

amino acids: _CA_, _CB_, _N__ 
pyrimidines: _C1*, _N1_, _C6_
purines: _C1*, _N9_, _C8_

 

Undo last mutation

  This option will restore the last residue to be mutated to its previous state.  

Undo TOR

  This option ``undoes'' the current TOR operation described above.  

Lock TOR

This option locks the current TOR operation, so that any future undo operation will return to this state, instead of the initial state.  

Undo FBRT

  This option ``undoes'' the current FBRT operation described above.  

Lock FBRT

This option locks the current FBRT operation, so that any future undo operation will return to this state, instead of the initial state.