UCSF-Chimera/C3/Build-Structures/English
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Slide Number 1
Title Slide |
Welcome to this tutorial on Build Structures. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
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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.
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Let us now start building a chemical structure using Build Structure tool.
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Cursor on Build Structure dialog box.
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A Build Structure dialog box opens on the screen.
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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.
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Click on atom.
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To build small molecules, click on atom radio button.
Atom parameters section opens.
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Click on Center radio button. | Click on Center of the view radio button, to place the helium atom at the center of the panel.
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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.
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A single Helium atom appears on the panel.
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Cursor on the panel. | Let us try to modify helium to a methane molecule.
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Click on element drop-down, select carbon.
Click on bonds drop-down, select 4. |
In the Build Structure dialog box;
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Cursor on the panel. | By default some of the parameters are already selected, leave them as such. |
Click on Apply.
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Click on Apply button.
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Click on selection tool, select clear selection.
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Using Select menu clear the selection.
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Hold CTRL key and click on any hydrogen atom. | Hold the CTRL key and click on any hydrogen atom on the methane structure.
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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.
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Click on Apply button.
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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.
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In Build Structure dialog box;
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Click on the fragment option.
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A Fragment library of various cyclic compounds is listed here. |
Click on 5-membered ring, select imidazole.
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Click on 5-membered rings.
Choose fragment from the list. I will choose imidazole.
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Cursor on the panel. | Imidazole molecule is displayed on the screen.
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Cursor on Active model bar.
Uncheck the box for model number zero.
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Uncheck the box for model number zero on the Active model status bar.
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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.
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We can join the two models on the panel;
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In the Build Structure dialog box, Click on other bond option. | Now the hydrogens are selected.
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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.
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Select Start Structure from the menu.
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Next let us create a peptide chain.
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Type,
ACDEFGH Click on Apply button.
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Type,
ACDEFGH
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Cursor on Add Peptide Sequence dialog box. | Add Peptide Sequence dialog-box opens.
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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.
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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
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A Dock prep dialog box appears on the screen.
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A Dock Prep dialog box appears, with model name.
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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.
Click on the radio button helical DNA/RNA. |
Type,
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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.
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A model of DNA as double helix displayed on the panel.
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Slide Number 5
Summary |
Let's summarize,
In this tutorial we have learnt to,
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Slide Number 6
Assignment |
For the Assignment,
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Slide Number 7
Acknowledgement |
* This video summarizes the Spoken Tutorial project
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Slide Number 8 | * We conduct workshops using Spoken Tutorials and give certificates.
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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. |