10.3 Atom Selection Tutorial

• Simple Atom Selection
• Atom Expression Field
• Select By Atom Types
• Select via Built-In Sets
• Select by Substructure
• Select by Monomer/Residue
• Select via Currently Defined Sets for Proteins

Setup

Clear the SYBYL screen of all molecules and background images.

   Edit > Clear All

   In the textport, type: take $TA_DEMO/tut.spl to load a dicloxacillin molecule.

Simple Atom Selection

   View > Display Style > Color > Atoms

The Atom Expression dialog is displayed. The option button in the upper left corner is set to Atoms, by default. Use this button to select various portions of a molecule (atoms or monomers).

   Click any five atoms in the work area.

Since the Highlight toggle button is On (the default), selected atoms are highlighted in green.

   In the Atom Expression dialog, press All.

All atoms are selected (and highlighted); the Selected information box at the top of the Atom Expression dialog shows that 49 atoms are selected.

Tip: If the Atom Expression dialog is hidden from view, click the icon.

   Press Clear.

The 49 atoms are no longer selected; Selected displays 0.

   Select three atoms.

   Press Undo to unselect the last selected item.

The Undo button enables you to "take back" the last operation.

   Press Invert to deselect atoms that were selected and select all others.

Selected displays 47.

   Press Clear.

Atom Expression Field

For the Atom expression field to be useful, you must first understand atom ID numbers and how SYBYL defines them.

   Click the icon and, in the M1 row, set the button in the Atm Lbl column to Id (press Close).

SYBYL identifies all atoms with a unique Atom ID number.

   Click one atom in the display area to select it.

SYBYL displays a green selection marker on the atom. The Atom expression field echoes the atom's ID number. If you continue to select atoms, each atom's corresponding ID number is echoed within the parentheses.

   Press Clear.

   Press All to select all atoms in the molecule.

An asterisk (*) appears between the parentheses, which represents all atoms in the molecule.

You can also type atom ID numbers, types, Boolean operators, and defined sets directly into the field.

   Replace * with 1+2+3.

   Press Apply.

Nothing happens until you press Apply. Three atoms are highlighted, since you asked for atoms that had the SYBYL IDs of 1, 2, and 3. The `+' signifies the "AND" (Union) Boolean.

   Press Clear.

Select By Atom Types

   Click the icon and, in the M1 row, set the button in the Atm Lbl column to Type (press Close).

   In the Atom Expression dialog, click Atom Types to display a predefined list of atom types.

   Check the N check box.

Several lines, representing all nitrogen atom types within SYBYL, are selected within the list.

   Press OK to return to the Atom Expression dialog.

The three nitrogens are highlighted. There are two types of nitrogens in this molecule: 2 N.am and 1 N.2.

So far, you have been able to add atoms to your selection because the Union operator is selected in the Atom Expression dialog.

Use the Difference operator, a subtraction Boolean, to keep the N.am atoms and turn off the N.2 atom.

   Change the Union operator to Difference (click to open the drop down options).

   Press Atom Types.

   In the Atom Types dialog, select N.2 in the list (press OK).

The N.2 atom is no longer selected, since the Difference operator was used to remove all N.2 atoms.

   Press Clear.

Select via Built-In Sets

SYBYL also has a wide variety of unique "Sets" available. Use sets to highlight unique characteristics of a molecule. Various built-in sets exist, including: Aromatic, H-bonds, Backbone, Sidechain, Rings, Bumps, and Metals.

A built-in set is a rule-based set, such as {AROMATIC}. For any molecule, SYBYL identifies the atoms belonging to this set when they are needed.

You are also able to select chirality sets and specify a sphere to select the molecules that are within the radius of the sphere.

1. Select all atoms that are aromatic.

   In the Atom Expression dialog, click Sets to open the Sets dialog.

   Click Aromatic to turn on the check box (press OK).

All carbons in the phenyl ring are selected and the Atom expression field has a defined argument to locate all (*) aromatic atoms, which is expressed as: {AROMATIC(*)}. (Set names must always be surrounded by braces.)

   Press Clear.

2. Locate all rings within this molecule.

   If necessary, on the Atom Expression dialog change the drop down option from Difference to Union.

   Press Sets.

   In the Sets dialog, check the Rings check box (press OK).

Four rings are identified and the Atom expression field has a defined argument to locate all atoms within a ring.

3. Find all nitrogen atoms in rings.

   In the Atom Expression dialog, change the drop down option from Union to Intersection.

The Intersection operator can be thought of as a true "AND" filter that must have both operations in common with one another. You have already selected Rings in the Atom Types dialog, now select another criteria.

   Press Atom Types.

   In the Atom Types dialog, check N (press OK).

Two nitrogen atoms are now selected. This is because two (of the three) atoms matched the intersection criteria (i.e., the atom has to be a nitrogen and be part of a ring).

   In the Atom Expression dialog, press Cancel.

Clear all molecules.

   Edit > Delete Molecule(s)

Select by Substructure

In the following steps load the crambin protein into SYBYL and color some of the substructures.

Note: There are many ways to display the Atom Expression dialog. Coloring atoms is the one used in this example.

   In the textport window, type take $TA_DEMO/tut_big.spl

   Click the icon and, in the M2 row, set the button in the Atm Lbl column to Substructure (press Close).

For biopolymers, each residue is a substructure. In the SYBYL window, the alpha carbon of each residue bears the label consisting of the amino acid name and ID number in the protein sequence.

   View > Display Style > Color > Atoms

   Press Substructures to open the Substructures dialog.

All substructures in the protein are listed.

   In the Residues list, select both A/THR1 and A/PRO41.

Note: For Linux users, to select more than one item from a list, Ctrl-click each item. For UNIX users, click each item.

Tip: You may need to scroll down the list to find A/PRO41.

   Press OK.

All atoms that are part of the two substructures are selected (green markers).

   In the Atom Expression dialog, press Clear.

Select by Monomer/Residue

   In the Atom Expression dialog, change the drop down option from Atoms to Monomers.

An additional field is displayed in the Atom Expression dialog, just above the molecule list. It lists the chains and the residues in each chain.

   In the new field that shows the chain, highlight CYS3-CYS4-PRO5.

Tip: As long as any portion of the residue's name in the list is highlighted, it is considered to be selected.

All atoms in the 3 selected residues are displayed with the green selection marker.

   Press Clear.

Note: You can also select residues via the Monomer Types button.

   Press Monomer Types.

   Select TYR in the list (press OK).

All tyrosines are selected.

   In the Atom Expression dialog, press Clear.

   In the Atom Expression dialog, change the drop down option from Monomers back to Atoms.

Select via Currently Defined Sets for Proteins

1. Color atoms that are in a helix and in the backbone.

   In the Atom Expression dialog, press Sets.

   In the Sets dialog, select HELIX_H1_PDB and HELIX_H2_PDB. from the list of Sets (press OK)

   In the Atom Expression dialog, change Union to Intersection.

   Press Sets.

   In the Sets dialog, click the Backbone check box in the list of Built-in Sets (press OK).

Only atoms that are part of the protein's backbone and in one of the two helices are highlighted.

   In the Atom Expression dialog, press OK.

   In the Option dialog, select MAGENTA (press OK).

All selected atoms are displayed in magenta.

2. Highlight the sheet in the protein.

   View > Display Style > Color > Atoms

   In the Atom Expression dialog, press Sets.

   In the Sets dialog, select SHEET_S1_PDB (press OK).

   Change Union to Intersection.

   Press Sets.

   In the Sets dialog, click Backbone (press OK).

   In the Atom Expression dialog, press OK.

   In the Option dialog, select GREEN (press OK)

The sheet is green.

3. Undisplay sidechains to have a better view of the protein backbone.

   View > Undisplay Atoms

   In the Atom Expression dialog, press Sets.

   In the Sets dialog, click Sidechain to turn on the check box (press OK).

   In the Atom Expression dialog, press OK.

4. List the sets you have made.

   Options > List > Sets

   Select CHAIN_HEAD.

SYBYL highlights the atoms that make up the CHAIN_HEAD set.

   Press OK.

   For Listing mode, select BRIEF (press OK).

Information about the CHAIN_HEAD set is displayed in the textport.

   Options > List > Sets

   Explore the other sets with the Select All, Invert, and Clear buttons.

   Press Clear (press OK).

5. Modify a set

   Edit > Modify > Set

   In the Option dialog, select NAME (press OK).

   Select CHAIN_HEAD (press OK).

   For the new name, enter: CHAIN_HEAD_tut (press OK).

6. Delete a set.

   Edit > Delete > Set

   Select CHAIN_TAIL (press OK).

SYBYL removes the molecules in the CHAIN_TAIL set.

7. When finished, reset the atom colors and Atom Expression dialog.

   View > Display Atoms

   Press the All button (press OK).

   View > Display Style > Color > By Atom Type

This concludes the Atom Selection Tutorial.

Crambin Protein Exercise

Using what you learned in this tutorial, clear the screen, load crambin, and do the following:

1. Color all atoms in external rings (sulfur) magenta.

2. Color all bonds connected to the sulfur atoms yellow.

3. Undisplay all external rings.

4. Change the remaining atoms to sticks.

Copyright © 2007, Tripos, L.P. All rights reserved.