Tutorial 1.

Dasar-dasar HyperChem
Pelajaran 1. Getting Started
Kemampuan yang diperlukan dalam Pelajaran ini.
• Menjalankan HyperChem
• Menggunakan mouse
• Mengidentifikasi bagian jendela HyperChem
• Menggunakan menu HyperChem
• Membuka file
• Melabel molekul
• Menggunakan molecular renderings
• Keluar dari HyperChem
Pelajaran 1 menjelaskan dasar-dasar HyperChem. Mula-mula anda jalankan program dan identifikasi
bagian jendela HyperChem. Pilih dan buka file yang mengandung jenis atom dan koordinat molekul
bentuk bola dari C-60, buckminsterfullerene.

Memulai HyperChem
Untuk memulai HyperChem:
1. Klik tombol Start, kemudian Programs, kemudian HyperChem Release 7. Anda akan melihat icon
gelas kimia hijau sebagai label HyperChem Professional. Klik pada item ini untuk memulai
HyperChem.

Parts of the HyperChem Window

Perlancar diri anda pada bagian bagian yang ada pada jendela HyperChem. Masing-masing item
dijelaskan pada bagian ini.
Title Bar
Title bar menunjukkan nama file yang sedang dikerjakan. Jika kita bekerja dengan suatu file yang belum
pernah disimpan, namanya terlihat sebagai untitled.
Menu Bar
Menu bar terdiri dari nama-nama menu HyperChem seperti: File, Edit, Build, Select, Display,
Databases, Setup, Compute, Annotations, Cancel, Script, dan Help.
Tool Bar
Bagian kiri dari Tool bar terdiri dari delapan tool icon yang dapat digunakan untuk mendraw, memilih,
menampilkan dan memindahkan/menggeser atau serta molekul. Pada tool icons terdiri dari:
menu bar, window border, title bar, status line, mouse pointer, workspace, Control-menu button,
minimize button, maximize/restore button, toolbar icons, Exit button, current calculation method
Empat dari tool icon dikanan berhubungan dengan anotasi. Disebelah kanannya lagi adalah toolbar icon
yang dipersiapkan untuk perintah singkat pada operasi seperti membaca dan menulis file, mengkopy dan
menpaste struktur, dan penggunaan bantuan on-line.
Ruangkerja(Workspace)
Ruang kerja adalah tempat HyperChem menampilkan sistem molekular yang sedang dikerjakan.
Status Line
Status line menunjukkan nomor atom dalam molekul yang sedang ditampilkan, status perhitungan, atau
nilai gradian atau energi. Bila kita memilih sutu menu, maka catatan singkat item ini terlihat pada status
line.
Help
Kita dapat menggunakan Help menu to untuk mengakses bantuan on-line.
Control Menu Button
Menu Control mengandung perintah-perintah merubah ukuran, memindahkan, memaksimalkan, dan
menutup jendela HyperChem. Juga mengandung perintah Switch, yang memungkinkankita
mengaktifkan jendela lain.
Maximize/Minimize Buttons
Tombol untuk mengembangkan ukuran kemaksimal. Beberapa jendela bisa berkembang cukup besar
dan ada juga Cuma sedikit. Kita dapat mengembalikan jendela keukuran awalnya dengan mengklik
kembali tombol Maximize.
Using the Mouse
Kita berkomunikasi dengan HyperChem umumnya menggunakan mouse, atau alat penunjuk lain
mengantikan mouse. Bila mouse digeser, kursor pada jendela juga bergeser. Kita berkomunikasi dengan
komputer dengan menekan tombol mouse. Berikut ini menjelaskan penggunaan mouse dalam
HyperChem:
Point Gerakkan mouse sehingga kursor penunjuk berada pada jendela HyperChem yang ingin dipilih.
Klik-L Tekan dan lepaskan tombol mouse kiri.
Klik-R Tekan dan lepaskan tombol mouse kanan.
Umumnya klik-R pengaruhnya berlawanan dengan klik-L.
Klik-Double Tekan dan lepaskan tombol mouse kiri dua kali dengan cepat.
Drag-L atau Drag-R Tekan terus tombol mouse kiri atau kanan dan geser ke posisi yang baru dalam
jendela kerja. Lepaskan tombol mouse.
Drag-LR Tekan terus tombol mouse kiri kemudian tombol mouse kanan selanjutnya geser ke posisi
yang baru dalam jendela kerja. Lepaskan kedua tombol mouse.
Drag-RL Sama seperti drag-LR, tetapi tombol mouse kanan yang duluan ditekan. Bentuk kursor mouse
berubah tergantung yang mana disorot dan mode HyperChem yang sedang jalan.

Untuk melihat kursor HyperChem berubah:

1. Sorot tool Drawing dan Klik- L.
2. Geser kursor ke ruang kerja (workspace).
Kursor berubah bentuk sebagai tool Drawing.
3. Sorot tool Selection tool dan klik-L.
4. Geser kursor ke ruang kerja. Betuk kursor berubah menjadi tool Selection.
5. Geser kursor ke menu Select pada menu bar.
Kursor kembali berbentuk panah.

Alternatif Keyboard
HyperChem menyiapkan pilihan keyboard standard Windows untuk digunakan sebagai mouse.
Untuk membuka suatu menu menggunakan keyboard:
1. Tekan terus [Alt] dan tekan kunci [S].
Menu Select terbuka.
Setiap menu pada title bar ada huruf yang digaris bawahi. Bila ditekan tombol [Alt] kemudian huruf ini
akan terbuka menu tersebut.
Menutup menu:
1. Tekan kunci [Alt] atau [Esc]. Menu Select tertutup.
Untuk memilih suatu menu:
1. Tekan terus tombol [Alt] dan tekan [S]. Menu Select terbuka.
2. Tekan [A]. Sama bila menggunakan mouse untuk memilih Atom pada menu Select.
Note: The HyperChem Release 5 for Windows Reference Manual lists keyboard alternatives.

Keyboard Shortcuts
HyperChem also has various keyboard shortcuts. Use the following shortcuts when you want to avoid
using the equivalent menus or menu items:
[Ctrl] + [N] Same as New on the File menu.
[Ctrl] + [O] Same as Open on the File menu.
[Ctrl] + [S] Same as Save on the File menu.
[Ctrl] + [X] Same as Cut on the Edit menu.
[Ctrl] + [C] Same as Copy on the Edit menu.
[Ctrl] + [V] Same as Paste on the Edit menu.
[Alt] + [F4] Same as Exit on the File menu
[Ctrl] + [D] Same as Delete on the Annotations menu.
[Ctrl] + [K] Same as Select Next on the Annotations menu.
[Ctrl] + [L] Same as Select Previous on the Annotations menu.
[Ctrl] + [F] Same as Move Forward on the Annotations menu.
[Ctrl] + [B] Same as Move Backward on the Annotations menu.
[Spacebar] Pressing the space bar is the same as using Scale to Fit on the Display menu. This menu item
centers and scales the molecule or selected items in the workspace.
[F2] Same as Last Rendering on Display menu.
[F3] Same as Show Isosurface on Display menu.
[F4] Same as Isosurface... on the Display menu.
[F9] Same as Copy Image on the Edit menu.
[Esc] Same as the Cancel menu item.
Opening a Sample File
You can work with molecules in tat least three ways using HyperChem:
• Using the tools and editing features, you create a two-dimensional (2D) sketch of a molecule, and then
convert it with the HyperChem Model Builder into a three-dimensional (3D) representation.
• Selecting residues sequentially from the HyperChem amino acid and nucleotide libraries to construct
proteins and nucleic acids.
• Reading in atom types and molecular coordinates that have been saved in the HyperChem input file
format (HIN file), the Brookhaven Protein Data Bank format (ENT file), or other file format. In this
exercise, to become more familiar with how HyperChem works, you read in molecular coordinates from
a HIN file.
To open a HIN file:
1. Move the pointer to File on the menu bar at the top of the HyperChem window.
2. L-click on File.
The File menu opens. An ellipsis appears after some menu items. This means a dialog box opens when
you choose these menu items.

3. L-click on Open.
The Open File dialog box appears:

Scrolling Through the List of Files

A list of files is located in the middle of the dialog box.
the ellipsis after a menu item means a dialog box appears when you choose the menu item

To scroll through the list:

1. Point the cursor on a scroll box and L-drag it up and down or left and right.

HyperChem scrolls through the list of filenames.

2. L-click on the up and down arrow keys to scroll one line at a time.
Changing Directories
If the file you want is not in the current directory, the Directories list box lets you change to a different
directory or disk drive.
Selecting a File
To select a file:
1. In the Files list box, go to the Samples/Aromatic directory and L-click on c60.hin. HyperChem
displays that name in the File Name text box.
Note: You can also enter a filename by entering it in the File Name text box. When a filename is
highlighted, any comments contained within the file appears in the Comments text box at the bottom of
the Open File dialog box. scroll boxes

2. L-click the Open button.

The dialog box disappears. The cursor turns briefly into an hour-glass icon to let you know that
HyperChem is reading in the file. As HyperChem reads the file, the number of atoms appears in the
status line at the bottom of the HyperChem window. The molecule appears:
Note: You can also open a file by double-clicking on a filename.

Using Display Settings

HyperChem automatically uses the display settings from the last session. You choose the display
settings by using menu items on the Display menu.
To open the Display menu:
1. L-click on Display on the menu bar. The Display menu opens:

Using Labels
If the molecule is displayed with labels, remove them using steps 1 and 2. Otherwise, skip to “To use
labels.”

To remove the labels:

1. L-click on Labels.
The Labels dialog box appears. Even if the currently displayed molecule is labeled, the dialog box opens
with the default setting of None for both atom and residue label types.
2. L-click on OK.
The dialog box closes and the labels are removed.

To use labels:
1. L-click on Labels.
The labels dialog box appears.
2. Choose Symbol as the atom label type, and then choose OK.
The dialog box closes and the molecule is labeled by atomic symbol.
3. Choose Labels on the Display menu.
Although the molecule is labeled, the dialog box opens with the default setting of None for both atom
and residue label types.
4. L-click on OK.
The dialog box closes and the labels are removed.

Using Different Molecular Renderings

You can use various molecular renderings when you display a molecular system.
To change the molecular rendering:
1. Choose Rendering on the Display menu.
The Rendering dialog box opens:

2. Choose Balls in the list, and then click on the “tab” at the top labelled Balls to show the Balls Options
property sheet:
3. If Shading is turned on (marked with a ✓), click on it to turn the option off (no ✓). Then choose OK.
This gives a crude, but quickly drawn, space-filled representation of the molecule. The molecule is
drawn using nonintersecting, nonshaded circles.

4. Reopen the Rendering dialog box. Choose Spheres, and then choose OK.

This gives a space-filled representation that simulates CPK models. It uses shaded spheres to represent
atoms and calculates intersections between bonded spheres.
5. Choose Rendering on the Display menu to open the dialog box once more.
6. Choose Sticks & Dots. Then choose OK to close the dialog box.
This representation gives you a good idea of the shape and volume occupied by the molecule.
7. Choose Rendering on the Display menu to open the dialog box once more.
8. Choose Balls and Cylinders. Then go to the Balls property sheet by clicking on the Balls tab at the top
of the dialog box, and turn on the Shading and Highlight options (both marked with ✓). Then choose
OK to close the dialog box.

9. Press the [F2] key to restore the previous rendering options. This is the equivalent of selecting Last
Rendering on the Display menu, and returns the display to the sticks and dots that were used before the
most recent change to the rendering options.
10. Open the Rendering dialog box again, choose Sticks, and then choose OK. The molecule appears in
its original stick rendering.

Exiting HyperChem
For now, exit HyperChem. To exit HyperChem:
1. Select Exit on the File menu.
If the program warns you about saving changes to the file, click on “No”. The window closes.

For More Information

For more detailed information on how to get started with HyperChem, see Chapter 1, “Introduction,” of
the HyperChem for Windows Reference Manual.
For information on how to use Microsoft Windows, see Help on the Start button.