UCSF-Chimera/C3/Build-Structures/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Build Structures.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to Create structures of small molecules, peptides and DNA fragments. Modify structure. Minimize energy, and Join models
Slide Number 3 Pre-requisites	To follow this tutorial you should be familiar with, Chimera Interface If not, for relevant tutorials, please visit our website.
Slide Number 4 System Requirement	To record this tutorial, I am using Ubuntu OS version. 14.04 Chimera version 1.10.2 Mozilla firefox browser 42.0 And a working Internet connection.
Double-click on the Chimera icon.	Here I have opened a Chimera graphics window.
Scroll down the Tools menu, select Structure editing option. From the sub-menu select Build Structure option.	Let us now start building a chemical structure using Build Structure tool. Click on Tools menu, scroll down to Structure editing option. From the sub-menu, click on Build Structure.
Cursor on Build Structure dialog box. Click on the Drop-down menu.	A Build Structure dialog box opens on the screen. Click Start Structure button available at the top of the dialog box.
Cursor on the menu.	Here we have options to build the structure from the scratch. We can also modify existing structure, adjust bonds, adjust torsions, join models etc.
Click on Start Structure.	Let's choose Start Structure option. Here, there are many options to start a structure. We can add atom, fragment, fetch a structure from Pubchem data base. Create peptide, DNA, RNA etc.
Click on atom. Click on Apply button.	To build small molecules, click on atom radio button. Atom parameters section opens. By default the structure begins with a helium atom.
Click on Center radio button.	Click on Center of the view radio button, to place the helium atom at the center of the panel. We also have options to input the X , Y and Z coordinates.
Click on “Select placed atom”	Click on Select placed atom.
In named text box type the name of the session as Sample-1. Click on Color new atoms by element. Click on Apply button.	In named text box type the name of the session as Sample1. Click on Color new atoms by element. Click on Apply button.
Cursor on the panel. Click on the Drop-down menu, choose Modify Structure.	A single Helium atom appears on the panel. Now we can modify this atom to any other molecule using Modify Structure option. Select Modify Structure option from the main drop-down menu.
Cursor on the panel.	Let us try to modify helium to a methane molecule. Let the helium atom be in the selection mode.
Click on element drop-down, select carbon. Click on bonds drop-down, select 4.	In the Build Structure dialog box; Change the element to carbon, bonds to 4 and geometry to tetrahedral. Hydrogens are attached as needed to satisfy the valency.
Cursor on the panel.	By default some of the parameters are already selected, leave them as such.
Click on Apply. Cursor on the panel.	Click on Apply button. Observe the panel. Helium atom is now replaced by Methane molecule.
Click on selection tool, select clear selection.	Using Select menu clear the selection. To further modify this molecule to Methyl amine, select any hydrogen atom.
Hold CTRL key and click on any hydrogen atom.	Hold the CTRL key and click on any hydrogen atom on the methane structure. Hydrogen atom is now selected.
In the “Modify Structure” dialog box; Change the element to nitrogen, bonds to 3 and geometry trigonal.	In the Modify Structure dialog box; Change the element to nitrogen, bonds to 3 , geometry trigonal.
Click on Apply. Cursor on the Panel.	Click on Apply button. Observe the panel. Amino group is now added to methane molecule. Clear the selection using Select menu.
Hold CTRL key and click on any atom or bond. Click on delete button in the Build Structure dialog box.	If you want to delete any atom or bond from the structure; Select the atom or the bond, click on delete button in the Build Structure dialog box.
Click on addh option in structure editing option in Tools menu.	To revert back to the original structure, add hydrogens using Tools menu.
Hold the center mouse button and drag.	Using the center mouse button, drag and place this model at the corner of the panel.
Cursor on Build fragment dialog box. Click on fragment.	In Build Structure dialog box; Click the drop-down menu and select Start Structure option. Now click on fragment radio button.
Click on the fragment option. Cursor on the drop-down menu.	A Fragment library of various cyclic compounds is listed here.
Click on 5-membered ring, select imidazole. Click on Apply.	Click on 5-membered rings. Choose fragment from the list. I will choose imidazole. Click on Apply button
Cursor on the panel.	Imidazole molecule is displayed on the screen. Move the imidazole molecule closer to methyl amine model.
Cursor on Active model bar. Uncheck the box for model number zero.	Uncheck the box for model number zero on the Active model status bar. This will make the amine model inactive on screen.
Click and drag the imidazole. Drop it close to amine model.	Using center mouse button move the imidazole closer to the amine model.
Click on the drop-down menu and choose Join Models option. Hold CTRL and Shift key and click on the any hydrogen atom.	We can join the two models on the panel; Using Join Models option in the Build structure dialog box. Select one hydrogen atom from each model where you intend to form a bond. Hold CTRL and Shift key at the sametime click on the hydrogen.
In the Build Structure dialog box, Click on other bond option.	Now the hydrogens are selected. Click on other bond option.
Click on Apply.	Information regarding the bonds is displayed on the dialog box. Click on Apply button.
Cursor on the panel.	Observe the panel, two models are joined.
Click on File menu, click on Close Session option.	Close the session using File menu. Click on the lighting bolt icon at the bottom of the window; to get back to graphics window.
Select Start Structure from the menu. Click on peptide option.	Next let us create a peptide chain. In the Build Structure dialog box, select Start Structure. Click on peptide radio button. In the Peptide Sequence text box, type the single letter code for amino acids. Let us type some random amino acid sequence.
Type, ACDEFGH Click on Apply button. Type model name as Sample-3.	Type, ACDEFGH The residues are added from N to C terminus. Type session name as Sample2. Click on Apply button.
Cursor on Add Peptide Sequence dialog box.	Add Peptide Sequence dialog-box opens. This dialog box is for specifying phi and psi angles.
Cursor on the dialog box.	By default phi and psi angles of -57 and -47 are displayed. These values correspond to a alpha-helix structure for the peptide fragment.
Cursor on the dialog box.	If you want to set the values, you can do so manually.
Cursor on the panel.	For now we will leave the phi\psi values unchanged. Click on OK button.
Cursor on the panel.	Observe the panel. We have a peptide chain displayed as helix.
On the command line. Type, minimize Press enter.	To minimize energy of the structure, type minimize on the command text box Press enter.
A Dock prep dialog box appears on the screen. Click on OK button.	A Dock Prep dialog box appears, with model name. By default some parameters are selected. For now we will not make any changes. Click on OK button.
Cursor on Add Hydrogens for Dock Prep dialog box.	This opens another dialog box to add hydrogens to the structure. A few parameters are already selected. Click on OK button. Observe the panel, hydrogens are added to the structure.
Cursor on Assign charges for Dock Prep dialog box.	Another dialog box opens, choose the force field package. By default AMBER ff14SB is selected for standard residues.
Click on OK button.	Click on OK button. It will take a few seconds to minimize the structure. Now on the panel we have a structure with most preferred conformation.
File menu >> Close Session.	Close the session using File menu and Open Graphics window.
Click on Add helical DNA/RNA.	Using the Build stucture tool, we can create a double helical DNA/RNA. On the Build Structure dialog box; Click on the radio button helical DNA/RNA.
Type, ATGAATGC	In the Sequence text box, type one letter nucleotide code for a DNA fragment. For demonstration I will type, ATGCATGC.
Click on DNA, B-form. Type the name as DNA-SAMPLE. Click on Apply button. Close the dialog box.	Click on DNA, click on B-form. Edit the name as Sample3 Click on Apply button.
Cursor on the panel. Click on Presets menu, choose interactive 2.	A model of DNA as double helix displayed on the panel. Change to atoms display using presets menu.
Slide Number 5 Summary	Let's summarize, In this tutorial we have learnt to, Create structures of small molecules, peptides and DNA fragments. Modify structure. Minimize energy, and Join models.
Slide Number 6 Assignment	For the Assignment, Join two benzene molecules to build a biphenyl molecule. Build a peptide fragment with your own choice of amino acid sequence. Build a RNA fragment with a random nucleotide sequence.
Slide Number 7 Acknowledgement	* This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
Slide Number 8	* We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
Slide number 9	The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

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Snehalathak