UCSF-Chimera/C3/Build-Structures/English-timed

Time	Narration
00:01	Welcome to this tutorial on Build Structures.
00:05	In this tutorial, we will learn to : create structures of small molecules, peptides and DNA fragments,
00:13	modify structure, minimize energy and join models.
00:19	To follow this tutorial, you should be familiar with Chimera Interface . If not, for relevant tutorials, please visit our website.
00:30	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.
00:48	Here, I have opened a Chimera graphics window.
00:52	Let us now start building a chemical structure using Build Structure tool.
00:58	Click on Tools menu, scroll down to Structure editing option.
01:04	From the sub-menu, click on Build Structure.
01:08	A Build Structure dialog box opens on the screen.
01:12	Click Start Structure button, available at the top of the dialog box.
01:18	Here we have options to build the structure from the scratch.
01:23	We can also modify existing structure, adjust bonds, adjust torsions, join models etc.
01:33	Let's choose Start Structure option.
01:37	Here, there are many options to start a structure.
01:41	We can add atom, fragment, fetch a structure from Pubchem data base,
01:48	create peptide, DNA, RNA etc.
01:53	To build small molecules, click on atom radio button. Atom parameters section opens.
02:01	By default, the structure begins with a helium atom.
02:05	Click on Center of the view radio button to place the helium atom at the center of the panel.
02:12	We also have options to input the X , Y and Z coordinates.
02:17	Click on Select placed atom.
02:21	In the named text box, type the name of the session as Sample1.
02:26	Click on Color new atoms by element.
02:30	Click on Apply button.
02:33	A single Helium atom appears on the panel.
02:37	Now we can modify this atom to any other molecule using Modify Structure option.
02:44	Select Modify Structure option from the main drop-down menu.
02:49	Let us try to modify helium to a methane molecule.
02:53	Let the helium atom be in the selection mode.
02:57	In the Build Structure dialog box,
03:00	change the Element to Carbon, Bonds to 4 and Geometry to tetrahedral.
03:08	Hydrogen atoms are attached as needed to satisfy the valency.
03:13	By default, some of the parameters are already selected, leave them as such.
03:20	Click on Apply button.
03:23	Observe the panel. Helium atom is now replaced by Methane molecule.
03:29	Using Select menu, clear the selection.
03:33	To further modify this molecule to Methyl amine, select any hydrogen atom.
03:39	Hold the CTRL key and click on any hydrogen atom on the methane structure.
03:46	Hydrogen atom is now selected.
03:49	In the Modify Structure dialog box, change the Element to nitrogen, Bonds to 3 , Geometry -trigonal.
03:59	Click on Apply button.
04:02	Observe the panel. Amino group is now added to methane molecule.
04:07	Clear the selection using Select menu.
04:10	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.
04:22	To revert back to the original structure, add hydrogens using Tools menu.
04:28	Using the center mouse button, drag and place this model at the corner of the panel.
04:35	In Build Structure dialog box, click the drop-down menu and select Start Structure option.
04:43	Now click on fragment radio button.
04:47	A Fragment library of various cyclic compounds is listed here.
04:52	Click on 5-membere rings.
04:55	Choose fragment from the list.
04:58	I will choose imidazole.
05:01	Click on Apply button.
05:04	Imidazole molecule is displayed on the screen.
05:09	Move the imidazole molecule closer to methyl amine model.
05:13	Uncheck the box for model number zero, on the Active model status bar.
05:19	This will make the amine model inactive on screen.
05:23	Using center mouse button, move the imidazole closer to the amine model.
05:29	We can join the two models on the panel, using Join Models option in the Build structure dialog box.
05:37	Select one hydrogen atom from each model where you intend to form a bond.
05:44	Hold CTRL and Shift key at the same time, click on the hydrogen.
05:52	Now the hydrogens are selected.
05:55	Click on other bond option.
05:58	Information regarding the bonds is displayed on the dialog box.
06:03	Click on Apply button.
06:05	Observe the panel, two models are joined.
06:10	Close the session using File menu.
06:15	Click on the lighting bolt icon at the bottom of the window to get back to graphics window.
06:22	Next, let us create a peptide chain.
06:25	In the Build Structure dialog box, select Start Structure.
06:30	Click on peptide radio button.
06:33	In the Peptide Sequence text box, type the single letter code for amino acids.
06:39	Let us type some random amino acid sequence.
06:43	Type: ACDEFGH. The residues are added from N to C terminus.
06:52	Type session name as Sample2.
06:56	Click on Apply button.
06:59	Add Peptide Sequence dialog-box opens.
07:03	This dialog box is for specifying phi and psi angles.
07:08	By default, phi and psi angles of -57 and -47 are displayed.
07:15	These values correspond to a alpha-helix structure for the peptide fragment.
07:21	If you want to set the values, you can do so manually.
07:26	For now, we will leave the phi\psi values unchanged.
07:30	Click on OK button.
07:33	Observe the panel. We have a peptide chain displayed as helix.
07:39	To minimize energy of the structure, type: minimize on the command text box. Press Enter.
07:48	A Dock Prep dialog box appears, with model name.
07:53	By default, some parameters are selected.
07:57	For now, we will not make any changes. Click on OK button.
08:02	This opens another dialog box to add hydrogens to the structure.
08:07	A few parameters are already selected. Click on OK button.
08:13	Observe the panel. Hydrogens are added to the structure.
08:18	Another dialog box opens. Choose the force field package.
08:24	By default, AMBER ff14SB is selected for standard residues.
08:31	Click on OK button.
08:34	It will take a few seconds to minimize the structure.
08:38	Now, on the panel, we have a structure with most preferred conformation.
08:45	Close the session using File menu and open Graphics window.
08:51	Using the Build stucture tool, we can create a double helical DNA/RNA.
08:57	Click on the radio button helical DNA/RNA.
09:01	In the Sequence text box, type one letter nucleotide code for a DNA fragment.
09:08	For demonstration I will type, ATGCATGC.
09:16	Click on DNA, click on B-form.
09:22	Edit the name as Sample3.
09:25	Click on Apply button.
09:28	A model of DNA as double helix displayed on the panel.
09:34	Change to atoms display using Presets menu.
09:39	Let's summarize. In this tutorial, we have learnt to: create structures of small molecules, peptides and DNA fragments,
09:49	modify structure,
09:51	minimize energy and join models.
09:55	For the Assignment- Join two benzene molecules to build a biphenyl molecule.
10:02	Build a peptide fragment with your own choice of amino acid sequence.
10:08	Build a RNA fragment with a random nucleotide sequence.
10:13	This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
10:21	We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
10:28	The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:35	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14