Use the Builder tool to create or modify the chemical system that is the basis for a calculation.
See also... | Builder Quick Reference - a one-page guide to the Builder interface |
To enter Select mode, click on the arrow button. In the work area, the mode label becomes "Select" and the cursor becomes the Select cursor (arrow). Other Builder tools that require atom selection (such as the measurement tools) also use the arrow cursor. The following are several ways to select atoms and bonds for operations in the Builder work area.
All these actions use the left mouse button. | ||
How to... | Instructions | |
Select an atom | Click on the atom. The selected atom is highlighted in fuschia. |
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Select all atoms in a rectangular area | 1. Position the cursor at one corner of the area. Depress
and drag in any direction. A rectangle forms with a fixed corner where you began the drag and the opposite corner following the cursor. 2. Release the mouse button to complete the selection. All atoms enclosed or touched by the rectangle are selected. |
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Select all atoms of a residue | Double-click on any atom in the residue. All atoms in the residue are selected. |
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Extend a previous selection | Depress the Shift key and use any of the selection methods above on unhighlighted
atoms. The new selection is added to the previous selection. |
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Select all atoms within a specific radius from one or more selected atoms. | 1. Select one or more atoms in the work area. The selected atoms are highlighted. 2. From the Edit menu, choose Select within radius. The Radius Selection dialog window displays. 3. Enter a radius (in Angstroms), and click the Select button. All atoms within that distance of any currently selected atom are added to the selection. To include any affected residues in the selection, even if some portions of the residues are outside the radius, first mark the Select complete residues option in the Radius Selection window. |
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Select all atoms in the work area | From the Edit menu, choose Select All. | |
Reduce a previous selection | Depress the Shift key and use almost any* of these selection methods
on highlighted atoms. The affected atoms are subtracted from the previous selection.
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Unselect all atoms in the work area | Click on any unoccupied space in the work area. Or if you are not in Select
mode, open the Edit menu and choose Unselect
All. All highlighted items return to their normal colors. |
Tip: The Geometry Table can be a handy way to select atoms while monitoring the details of the chemical system. By selecting rows (atoms or bonds) in the Geometry Table, you also select the corresponding atoms in the Builder work area. |
Use the Edit: Select Within Radius window to select all atoms or residues within a defined radius of currently selected atom(s).
Radius selection can be based on a single atom or a set (multiple atoms) of atoms. Any non-highlighted (unselected) atom that is within the specified radius of any of the highlighted atoms will be included in the radius selection results. The Select Within Radius option defines the distance, from any of the highlighted atoms, to use for the radius select search.
If Select Complete Residues is indicated, then all atoms of a residue will be included in the radius selection results if one or more of its atoms are within the specified radius.
Select an atom or multiple atoms in the molecule.
From the Builder's Edit menu or the Calculation Viewer's Edit menu, choose Select Within Radius.
The resulting options window displays the current settings and controls.
Enter a radius in angstroms.
To select complete residues, click the Select complete residues checkbox.
Click the Select button to select all the atoms within the specified distance of any currently selected atoms. If the "Select complete residues" toggle is set, then all atoms in any residue that was within the specified distance will also be selected. The centers of atoms must be within the radius to be selected.
Selection Options | |
Radius | Select all atoms that are within the specified distance (radius) of any currently selected atom. |
Select complete residues | Selects a volume encompassed by the radius you set, and will include the complete residue beyond the specified radius. All atoms in any residue that has at least one atom within the specified distance will be selected. |
Note: You can also hide selected atoms or modify their depiction in the Builder's work area by using the Style (Selected) option on the Builder's Display menu. |
The new atom is added at the specified location. As long as the Builder remains in "Atom" mode, each click of the mouse will add a new atom in the work area.
See also... | Modify Atoms and Bonds |
Tip: If the atoms added to the work area appear too small, open the Options menu and mark Autonormalize Display. Each time you add an atom, the Builder will recenter and rescale the chemical system. |
To add hydrogens at all unoccupied bonding sites (nubs):
To use elements and bond geometries that do not appear in the basic palette:
Picture... | More Elements and Bond Geometries |
To automate Builder tasks by recording and replaying a sequence of Builder commands:
From the File menu, choose Undo [last operation]. The Builder keeps track of your last 10 operations, which you can undo, one by one.
From the File menu, choose Save (or click on the star-shaped "Save Work" icon ). This saves the chemical system as part of the current calculation.
If you launched the Builder directly from the Gateway, the Save option will be disabled because there is no specified calculation to which the chemical system can be saved. In that case, you can either drag a molecule from the Builder onto the drop site in the Calculation Editor or use the File menu Save As option to save the chemical system in a new calculation.
See also... | How to export a chemical system to a molecular modeling format (and save a chemical system when using the standalone Ecce Builder) |
How to add molecular structures to a Structure Library |
Picture... | Structure Library Window |
More about... | Structure Libraries |
Tip: If the Structure Library window appears disabled (grayed out), you have switched to a different mode. To enable the Structure Library and return to "Add Structure" mode, just click again on the Structure Library button in the Builder window. |
To replace one atom with another:
To replace all hydrogens with empty nubs:
You can change the location of objects in the Builder's work area by two methods: move your viewpoint (change your camera angle) or move the objects (change their space coordinates). The difference may not be important unless you are trying to build a structure based on space coordinates.
To move your point of view:
The cursor switches to the Manipulate cursor (hand) in the work area. |
The cursor switches to the Translate cursor (hand with object) in the work area. |
The cursor switches to the Dolly cursor (pointing hand) in the work area. |
To move and rotate objects in space:
Picture... | Manipulator Sphere |
To move atoms in space | Click on the gridded surface of the manipulator sphere. While the mouse button is depressed, a double-ended arrow will appear through the center of the sphere, indicating the directions in which you can now drag and move the enclosed atom(s). It may take a bit of practice to become accustomed to using these manipulators. |
To rotate atoms in space | Click on one of the two green bands that around the manipulator sphere. While the mouse button is depressed, you can rotate the sphere and the enclosed atom(s) along the direction of the selected band. |
To rotate atoms about a bond axis:
Picture... | Manipulator Wheel |
To improve the structure of molecules that have been built by hand, click on the Clean (broom) icon. This applies a simple molecular mechanics force minimization based on the Universal Force Field (UFF) of Rappe and Goddard.
The results of this operation are affected by the initial shape of the structure. You can also set parameters for this operation. The speed of this operation depends on the number of atoms. If no atoms are selected when the clean button is activated, then all atoms are optimized. If a subset of atoms is selected, then only the coordinates of the selected atoms are updated, although the remaining atoms are included when evaluating the forces on the atoms. The clean function can be slow for large systems, even if only a few atoms are selected.
Tip: Be careful using "Clean" on a molecule that has empty bonding site nubs because the nubs may end up being obscured by other structures after the clean operation. You may want to use the Add H button to add hydrogens to empty nubs before using the Clean icon. |
You can import molecular structures directly to the work area of the Builder or to a selected folder in the Structure Library. You can export structure files or graphic files from either the Builder or the Structure Library.
To import molecular structures:
Picture... | Import Dialog Window |
To export molecular structures:
Picture... | Export Dialog Window |
Structure libraries are folders of the Ecce Web server, typically created to store only chemical systems without any related information. You can create new structure libraries that contain up to about 20 structures in each folder. You can delete only structure library folders that you have created.
Note: Standalone Molecule Builder--The Structure Library files are included with the standalone Builder installation under the data/client/StructureLibrary directory rather than located on the Ecce Web server. |
Picture... | Structure Library Window |
More about... | Structure Libraries |
To add molecular structures to the new structure library:
To delete a structure library:
Use the Details: ChemSys Display Options window to adjust the appearance of atoms and bonds. The visible effect of the window controls depends on the general display style already in effect (Ball & Stick, Stick, Ball & Wireframe, Stick, Wireframe, or CPK).
Picture... | Chemical System Display Options Window |
From the Builder's Display menu or the Calculation Viewer's Chemical System menu, choose Render Quality and then Customize.
The resulting options window displays the current settings and controls. All controls in the window are either exclusive options or range sliders. Most sliders are marked from 1 to 100% with corresponding dynamic readouts from .01 to 1.0 .
To adjust a display attribute, mark the option box or drag the range slider using the left mouse button.
Wire Options (chemical system appearance for Wireframe styles) | |
Line Width | Width of the lines used for wireframe from about 1 to 10 pixels (.01 to .10). |
Cylinder Options (bond appearance for Stick styles) | |
Cap Style | Appearance of the atom ends of the bonds (Caps appear only in Stick style.) |
Render Quality | The stick quality modifies the stick cross section from nearly triangular (0.1) to circular (1.0). |
Radius | Radius of sticks |
Sphere Options (atom appearance for Ball and CPK styles) | |
Hemi Spheres or Full Spheres | Full Spheres is the preferred option for most workstations. The Hemi Spheres option may increase display speed, but the display can be uneven. |
Render Quality | The sphere quality modifies the rendering from an 8-faced cube (.01) to an n-faced polyhedron approximating a sphere (1.0) The default sphere quality is set at about 50% (0.5). Higher values will increase the graphic quality and rendering time for atom surfaces. |
Ball/Stick Scale | Relative size of the spheres from near zero (.01) to normal (1.0) |
Note: You can also hide selected atoms or modify their depiction in the Builder's work area by using the Style (Selected) option on the Builder's Display menu. |
From the File menu, choose Print. In the resulting window you can select from a scrolling list of available printers.
Ecce Online Help Revised: April 29, 2004 |
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