Structure files

Pronto is capable of reading structure files. Two types of PDB files can be read:

1. "Real" PDB files. Atoms are named according to the PDB conventions, and substructures within the file are separated by MODEL record.
2. PDB files generated by X-PLOR.

This chapter describes the following topics:

1. Reading and writing PDB files
2. Displaying structures

Reading and writing PDB files

The structure cluster catalog is opened from the Data menu. An example is shown in Figure 1. Each structure cluster can contain one or more substructures. To read in a new structure, press New and Read.

Figure 1: The structure cluster catalog.

Pressing Zoom in the structure cluster catalog window opens a window giving detailed information about the substructures. It is possible to select/deselect entries used in the subsequent display of structures.

Figure 2: The structure cluster read menu. The file selected must be a "real" PDB file. If it contains several substructures, all will be read in. If file format is set to X-PLOR (PDB), each substructure is contained in a separate file. Select a file name like "/indy2/mk/accept_%d.pdb", set first structure number to 1, and last structure number to the number of substructures to be read.

The substructure cluster reader is shown in Figure 2. Reading in a lot of substructures can make your database grow quite large. If you delete structures from the database, you must export the database in ASCII, and reimport it. See here how to do it.

The structure cluster catalog window also contains tools for exporting PDB structures. It is thus possible to import files in X-PLOR PDB format and export them into a single, "correct" PDB file. However, the program still has some problems in setting the atom names correctly in the PDB file.

Selecting a cluster in the Structure Cluster window makes Pronto read in all the atom coordinates from the database into memory. This can take some time. Bonds are generated between atoms that are within Van der Waals contact plus 0.25Å, if the atoms belong to residues that are adjacent in the sequence or cysteins.

Displaying structures

The display of structures works best on a Silicon Graphics machine (GL). If a GL driver is not found, X-Windows is used instead. This may give some colormap flashes in the other windows when the molecule is rotated. Stick models work best in X-Windows.

Figure 3: The structure display window.

The structure display window is shown in Figure 3. The list at the top shows various stored setups. To store a new entry in the list, insert the desired name in the field below the list and press Save. Press Load to restore a setup, and Insert to merge a stored setup into the current setup.

The bottom list is the actual setup. Each setup displays a set of atoms from a specific structure cluster in a specific way. To have atoms displayed in several ways simultaneously, create several setups that only differs in the way the atoms are displayed.

Press Update Display to display the structures. The mouse is used to control the orientation of the molecule. Press Reset View to center the view on the display. The current transformation matrix is stored in the setup list.

The mouse operates in the following way in the structure display window:

• Left button drag: Rotate around X- and Y-axes
• Middle button drag: Translate in X- and Y-direction
• Left and right button drag: Rotate around Z axis
• Left and middle button drag: Translate in Z axis
• Middle and right button drag: Zoom in or out
• Click right button: Select atom. Only assigned atoms can be selected!

The entries at the bottom of the window selects the output format for ray traced images. Pronto can prepare input files for POVRAY and Rayshade. Insert the file name at the bottom. Pressing export in the structure display window exports the displayed items to the raytracer in the current view.

Setting up the structure display

Figure 4: Structure display setup. Plot a green ribbon.

The setup shown in Figure 4 selects structure cluster no. 0, displays all atoms as a ribbon, in green.

The atom selection is a Boolean expression. The syntax in Backus-Naur Form is as follows:

1. <atom selection> :== <expression>
2. <expression> :== <term> {OR <term>}
3. <term> :== <factor> {AND <factor>}
4. <factor :== ( <expression> ) | NOT <factor> | BYRES <factor> | <element> AROUND <distance>
5. <element> :== SEGID <chain id> | RESID <residues> | RESNAME <residue name> | CHEMICAL <atomic element> | NAME <atom name> | HYDROGEN | ALL | ASSIGNED | ATID <at number> | CURAT | PREVAT | CPA1 | CPA2 | CPA3 | CPA4
6. <residues> :== <number> | <first>:<last>

Some of the elements may need further description:

BYRES <factor>

If <factor> selects an atom from a residue, then the rest of the atoms in that residue will be selected as well.

<element> AROUND <distance>

Selects atoms that are within <distance> Å from any atom in <element>.

ASSIGNED

Select assigned atoms

ATID <at number>

Select atom in structure assigned to a specific entry in the Pronto atom catalog.

CURAT

Select atom in structure assigned to the currently selected entry in the Pronto atom catalog.

PREVAT

Select atom in structure assigned to the previously selected entry in the Pronto atom catalog.

CPA1 | CPA2 | CPA3 | CPA4

Select atoms selected in one of the four axes in the active Cross Peak Assigner window.

Pronto supports the following ways of displaying structures:

• Bond display. A line is drawn between atoms. The bonds can be drawn in a specific color, or if the color is set to white, the bonds will be colored according to the atom type. Line width and line types (solid, dotted, etc.) can be set.
• Sphere display. Each atom is displayed as a sphere. The field: Line width sets the percentage of the Van der Waals radius to display.
• Ribbon. Calculate a smoothed ribbon. See Figure 5.
• Helix. Fit a helix. You should only select residues that actually exist in helix structures for this mode. Included in Figure 6.
• Sheet. Fit a beta-sheet to the atoms. Select only residues in beta sheet structure.
• NOE display. Plot lines between atoms linked by NOE assignments. This could be slow, as it has to go through the whole Pronto data base.
• Text labels. Put a text label on the selected atoms.
• Worm and Fribbon: Other ways of displaying ribbon.

Figure 5: Ribbon display. The result of the setup in Figure 4.

Figure 6: Ribbon and helix. You would have to specify the helix ranges manually!

Figure 7: Ribbon, helix, and spheres. The SEGI selection is used to select the ligand segment for the sphere display.

Figure 8: Bond display. The fastest display type.