UCSF-Chimera/C2/Picking-and-Selection/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Picking and Selection using Chimera.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to Show labels for atoms and residues. Select atoms and residues using Select menu or by Picking. Change the color and display of the residues. Add, delete or change atoms Rotate bonds
Slide Number 3 Learning Objectives	* Open more than one model on the display window. Select and move the model.
Slide Number 4 Pre-requisites	To follow this tutorial you should have knowledge of Undergraduate Biochemistry. Or familiar with structural biology. For relevant tutorials, please visit our website. http://spoken-tutorial.org
Slide Number 5 System Requirement	To record this tutorial, I am using, Ubuntu Operating System version. 14.04 Chimera version 1.10.2 Mozilla firefox browser 35.0 And a working internet connection.
Click on the UCSF Chimera icon to open the Chimera window. Click on “1zik' on the rapid access window.	Here I have opened a Chimera window. On the rapid access window, click on 1zik from the list of recently accessed data. A model of Leucine zipper opens on the graphics window.
Cursor on the panel.	Individual components of the structure such as: residues, atoms, bonds etc can be modified using tools available in Chimera. The first step is to make selection.
Slide Number 6 Ways to make a Selection	There are different ways to make a selection: using the Select menu in the menu bar. Picking from the graphics window. Typing commands on the command line. Or by selecting, Model Panel and Sequence option present in the Favorites menu.
Cursor on the panel.	Back to the Chimera window. Leucine zipper motif consists of periodic repetition of leucine residues. I will now demonstrate how to highlight the leucine residues present in this structure.
Click on presets option in the tool bar. Click on interactive 2. Scroll down the Select menu.	From the presets menu choose interactive 2 option. This will convert the structure to atoms display. From the Select menu choose Residue option. The sub-menu has many options.
Cursor on the menu.	The Amino acid category menu has amino acids grouped as: aliphatic, aromatic, hydrophobic, polar etc.
Cursor on the menu. Click on leucine.	Standard amino acid menu has list of amino acid residues present in the structure. Click on leucine. All the leucine residues are now highlighted.
Click on actions menu, select color, choose yellow. Cursor on the structure.	Click on actions menu, select color. I will choose yellow from the list of colors. All the leucines are now displayed in yellow color.
Click on Select menu. Click on Clear selection option.	To clear the selection, click on Select menu. Then click on Clear selection option.
Cursor on the window.	Leucine being hydrophobic is packed into the hydrophobic core of the protein.
Scroll down the presets menu. Click on Interactive 1.	Now change the display to ribbons using presets option. Click on Interactive 1.
Place the mouse anywhere on the structure. Hover the cursor over the structure.	To pick a residue from the screen : Hover the cursor over the structure.
Cursor on the pop-up balloon.	A pop-up balloon appears with identifying information. It has information such as residue name, residue number and Chain.
Move the cursor.	The balloon disappears when you move the cursor.
Bring the cursor to the first residue on chain A.	Bring the cursor to the first residue on chain A, that is arginine.
Press CTRL key on the keyboard and click.	Press and hold the CTRL key on the keyboard and click the left mouse button. Release the CTRL key.
Cursor on the structure.	The outline of the residue is highlighted. By default the selection is outlined in green.
Press and hold both CTRL and shift key. Click on the residues.	If you want to select more than one residue; Press and hold both CTRL and shift key on the key board. Hover the mouse over the peptide chain. Click on the residues you want to pick. Release the CTRL and Shift keys from the key board.
Cursor on the structure.	Now you have picked the residues for modification.
Click on Actions menu. Scroll down and click on atoms/bonds. Click on “show”.	Choose an option from the Actions menu. Click on Actions menu. For example to display atoms, choose atoms/bonds. Click on Show.
Cursor on the structure.	The selected residues are now seen in atoms display. Clear the selection.
Cursor on the structure.	We can also modify atoms or bonds present in the structure by Picking.
Place the mouse over an atom and bond.	Place the cursor over an object such as an atom, or bond. This will show its label information in an atomspec balloon.
Cursor on the panel.	Atomspec balloon for an atom has information such as: Residue name, number, chain and atom name.
Double-click on the atom, while holding down the CTRL key. Scroll down the context-menu.	To select an atom, press and hold the CTRL key on the key board. While holding the CTRL key click on the atom you want to change.
Cursor on the structure. Double-click on the atom while holding the CTRL key.	The atom is now highlighted. To modify the atom double-click on the atom while holding the CTRL key.
Cursor on the context-menu. Click on Modify-atom option. Release the CTRL key.	A context menu opens with options. Click on Modify-atom option. Release the CTRL key.
Click on modify atom, a “Build Structure” window opens.	A Build Structure window opens. Let us change the selected atom that is Nitrogen to a methyl group.
Select carbon, 4 bonds, click on apply.	In the Build Structure window, Select element as carbon, bonds as 4. Click on apply button. Observe the panel. A methyl group is now added to the existing structure. Close the window.
Hover the cursor on any bond. Cursor on the pop-up balloon.	There is also an option to rotate bonds. Hover the cursor over the bond you want to rotate. Information regarding the bond appears in the atomspec balloon.
Press CTRL key and click on the bond.	To select a bond, place the cursor on the bond. Press and hold the CTRL key. Click the left mouse button.
Cursor on the bond. While still pressing the CTRL key double click on the bond.	The selected bond is now highlighted. While still holding the CTRL key double click on the bond. Release the CTRL key on the key board.
Click on rotate bond option in the context menu.	A context-menu opens. Click on rotate bond option. A Build Structure dialog box appears on the screen.
Click and rotate the rotating tool that is present in the dialog box.	Click and rotate the rotating tool that is present in the dialog box. Observe the panel. The selected bond is now rotating. Stop rotating when you reach the desired angle. Close the dialog box.
Hold the CTRL key and click anywhere on the panel.	Clear the selection.
Scroll down the tools menu and click on “Sequence” option.	We can also use Sequence option in the tools menu to highlight the chains. Scroll down the tools menu and click on Sequence option. Choose Sequence from the sub-menu.
Cursor on the dialog box. Click on chain A, then click on show button. Cursor on the dialog box.	A Show model sequence dialog box appears. Click on chain A if you want to select chain A. Then click on show. Another dialog box appears on screen with the amino acid sequence.
Cursor on the dialog box.	The amino acid residues are represented as single letter abbreviations. Click on the sequence to select.
Click on quit to close the window.	Observe the panel, Chain A is now highlighted. Click on quit to close the window.
Go to action menu, scroll down to color. Click on yellow.	Go to Actions menu, scroll down to Color. Click on yellow option. Chain A is now in yellow color. Clear the selection.
Cursor on the window.	We can open more than one structure on the Chimera window.
Scroll down the file menu, Click on “Fetch by ID”. “Fetch structure window”, select PDB option.	To open a second structure: Scroll down the file menu. Click on Fetch by ID. A Fetch structure by ID dialog box opens. Select PDB option.
Type the 4 letter PDB code. 2HCO and click on fetch button. Click on fetch button.	Then type the 4 letter PDB code. For example to fetch human insulin, type 4ex1. Click on fetch button.
Cursor on the panel.	The two protein structures are overlapped on the panel.
Cursor on the panel.	To separate the two overlapping structures: We have to selectively move one model on the panel.
Click on favorites menu. Scroll down and click on Command line option. On command line, Click on the small square box for zero.	Open the Command line using favorites menu. The Command line appears at the bottom of the window. Click to uncheck model zero, which represents leucine zipper.
Hold center mouse button move the second model on the panel.	Bring the cursor to the insulin structure: Hold the center mouse button. Drag to move the insulin model to the desired location on the panel. Release the mouse button.
Open the model panel using favorites menu. Clicking on the model ID.	To selectively remove model from the screen: Open the model panel using Favorites menu. A Model Panel dialog box appears.
Cursor on model panel dialog box.	Select the model you want to remove, by clicking on the model ID. For example I want to remove the insulin model from the screen.
Click on the model ID. Click on close option.	Click on the model ID. Click on close option.
Click on close.	Observe the panel. The model of insulin is now removed from the screen. Close the model panel window.
Cursor on the panel.	We have reached the end of this tutorial.
Slide number 7 Summary	Let's summarize what we have learnt.
Slide Number 7 Summary	In this tutorial we have learnt to Show labels for atoms and residues. Select atoms and residues using Select menu or by Picking. Change the color and display of the residues. Add, delete or change atoms Rotate bonds
Slide Number 8 Summary	* Open more than one model on the display window. Select and move the model.
Slide Number 9 Assignment	For the assignment Open a structure of human insulin, pdb code 4ex1 on the Chimera window. Color all the hydrophobic amino acid residues in blue. Color all polar residues in red. Your completed assignment should look as follows.
Slide Number 10 Acknowledgement	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 11 Acknowledgement	The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.
Slide number 12 Acknowledgement	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available at the link shown
Slide number 12 Acknowledgement	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Snehalathak