Difference between revisions of "UCSF-Chimera/C4/Axes-and-Planes/English"

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to show,
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to show,
  
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'''Axes''', '''Planes''' and '''Centroids'''
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'''Axes''', '''Planes''' and '''Centroids'''
  
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'''2D Labels''' and
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'''2D Labels''' and
  
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'''Per-Model clipping'''.
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'''Per-Model clipping'''.
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''
 
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'''System Requirement'''
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial, I am using,
  
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Tools''' menu, scroll down to '''Utilites.''' Choose '''2D labels '''from the sub-menu.
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Start '''2D labels''' tool using''' Utilities''' option from the '''Tools''' menu.
  
 
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By default '''use mouse for label placement'''option near the bottom of the dialog box is selected.
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change thickness, click on '''Adjust clipping with mouse'''.  
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Select button 2 for Translation.
 
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'''Acknowledgement '''
 
'''Acknowledgement '''
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * This video summarizes the Spoken Tutorial project.
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If you do not have good bandwidth, you can download and watch it.
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This video summarizes the Spoken Tutorial project.
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If you do not have good bandwidth, you can download and watch it.
  
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We conduct workshops using Spoken Tutorials and give certificates.  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We conduct workshops using Spoken Tutorials and give certificates.  
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Please contact us.
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Please contact us.
  
 
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Latest revision as of 11:59, 2 November 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Axes and Planes using Chimera.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to show,

Axes, Planes and Centroids

2D Labels and

Per-Model clipping.

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 1.10.1

Mozilla firefox browser 42.0, and

working Internet connection.

Double-click on Chimera icon. Here I have opened Chimera window.
On the command text box type 1EMA. On the command text box type,


open 1EMA

Press enter

Cursor on the panel. Structure of green fluorescent protein opens on the panel.
Click on Tools menu. Scroll down to Structure Analysis option.


Click on Axes, Planes and Centroids

Click on Tools menu.


Scroll down to Structure Analysis option.


From the sub-menu click on Axes, Planes, Centroids.


Structure Measurements dialog box opens.


Here we have Define axes, Define plane, Define centroid tabs.

Click on Define axes button.


Click on Define axes tab.


This opens Define axes dialog box.


Here we can specify atom sets and other axis parameters.

while holding CTRL and shift keys, click on atoms. On the panel, select a few residues of your choice, from the middle of the structure.


To select residues;


Click on residues while pressing CTRL and shift keys simultaneously.

Click on the radio button “Selected atoms” On the Define Axes dialog box, click on the radio button “Selected atoms”
Type “axis1”. Type the name of the axis as axis1.
Click on the color well.

Select a color from the color editor.

Click on the color well.

Select a color from the color editor.

Close the color editor.

Click on OK button. To change the thickness of the axis;


click on angstroms radio button.


Change the number in the text box to 0.25


Click on OK button.

Cursor on the panel. Observe the panel.

Axis is drawn for the selected atoms.

Clear the selection using select menu.
An object for this axis is generated in the Structure Measurement dialog box.
Click on row with the name of the axis.

Click on delete button at the bottom of the window.

To delete axis, click on the row.


Click on Delete button at the bottom of the dialog-box.

Click on Define plane button. Now to add plane to the structure, click on Define plane tab.


In the Define Plane dialog-box, change the name of the plane to plane1.

Cursor on Define Plane dialog-box. Here a plane is created only for selected atoms.
Hold the CTRL key and click on 3 or more atoms in a row on the ligand. On the panel;

Select few residues of your choice, from the middle of the structure. Press CTRL and Shift keys simultaneously and click on the residues.

In the Plane name text box, type Plane1.

Click on the color well, In the color editor dialog-box, select color of the plane.

On the Define Plane dialog-box;

Click on the color well.

Choose a color from the color editor.

Close the color-editor.

Click on OK button. Click on OK button.

Observe the panel.

Cursor on the panel. A plane is generated based on the selected atoms.


Clear the selection using Select menu.

Click on the plane ID in the Structure Measurements dialog box.

Click on delete.

Delete the plane, click on the plane ID in the Structure Measurements dialog box.

Click on delete button.

Click on Define centroid button. To show centroid, click on Define centroid tab.


Define centroid dialog box opens.

Select residues 64 and 68. Select residues 64 and 68 on the structure to create a centroid.



Type the name of the centroid as centroid1. In the Define Centroid dialog box;


type the name of the centroid as centroid1.

Select the color from the color well.

Click on OK button.

As shown earlier, select a color from the color well.


Close the color-editor.

Click on OK button.

Cursor on the panel. Centroid for the chosen atoms is displayed on the panel.


Clear the selection and delete the centroid.


Close the Structure Measurements dialog box.

Cursor on the panel. 2D-Labels such text and arrows can also be added to the structure.
Click on Tools menu, scroll down to Utilites. Choose 2D labels from the sub-menu. Start 2D labels tool using Utilities option from the Tools menu.
Cursor on 2D-Labels dialog-box. 2D-Labels dialog-box opens with tabs for Labels, Arrows and color key.
Click on Labels tab. Click on Labels tab to add labels.


By default use mouse for label placement option near the bottom of the dialog box is selected.

Click on the color well.

Drag the slider to select color.

Close the color editor.

Click on the color well, select a color for the label.

Close the color editor.

Click on the panel. Click on the panel where you want to place the label.
Cursor on 2D-Labels dialog-box. Label id with X and Y coordinates appears on the dialog-box.
Type Green Fluorescent Protein in the Text area.


Press enter.

Now type the label text in the Text area.


Type Green Fluorescent Protein.


Press enter.

Drag the symbol using left mouse button. The label created can be repositioned by dragging using left mouse button.
Select label id on the dialog-box.

Click on delete button.

To delete the label, select the label id on the dialog-box.

Click on delete button.

Click on Arrows button. Click on Arrows tab in the dialog-box to add arrows.
Type 0.5 in arrow weight text box.


Click on the Arrow head style button.

In the Arrow weight field at the bottom of the dialog-box;


Change the number to change the thickness of the arrow.

I will type 0.5 to create a thinner arrow.

Click on the Arrow head style button.

Choose an option from the drop-down menu.

I will choose Pointy.

Place the cursor on the panel, click, hold the mouse button. Drag to extend the arrow.

Release the mouse button.

Place the cursor on the panel, click and hold the mouse button.


Drag to extend the arrow.


Release the mouse button.

Drag the end of the arrow.


Place the cursor in the middle of arrow and drag.

Drag the end of the arrow to reorient or to change its length.


Move the arrow by dragging it from the middle.

Click on the color-well.

Drag the slider and choose color.

Change the color of the arrow by clicking on the color well next to the arrow id.


Select a color. Close the color-editor.

Close the 2D-Labels dialog-box. Close the 2D-Labels dialog-box.


Close the session using File menu.


Open a new session.

Type, open 1MBO. To demonstrate per-model clipping;


I will use structure of myoglobin as an example.


On the command text box type open 1mbo.


Press enter.

Scroll down Tools menu, select Depiction.

Select Per-Model clipping.

Scroll down the Tools menu, select Depiction.

From the sub-menu, click on Per-Model clipping.

Cursor on Per-Model clipping. Per-Model clipping dialog-box opens.
Slide number 5

Per-Model Clipping

Per-Model Clipping allows different models to be clipped in different ways.

It is a single plane that separates the visible and invisible portions of the model.

Slide number 6

Per-Model Clipping

Each model can have only one Per-Model Clipping plane.

A model and its surface are treated as separate models.

Click on Actions menu. Back to the panel.

Model drop-down menu in the Per-Model Clipping dialog-box shows the current model.

Click on radio button Enable clipping. Select Enable clipping, this activates the clipping planes.
Rotate the model using mouse. Visible portion of the model is behind the plane.

Uncheck Enable clipping.

Select Surface, click on show. Create a surface for the model.

Click on Actions menu, scroll down to Surface.

Click on Show.

Point to the pocket. Now the structure shows a pocket where Heme group is bound tightly.
Click on Model tab. In the dialog-box, Model drop-down menu, shows two models.

Model (1mbo) and

Model with surface.

Click on model id. Select model with surface.

Click on Enable clipping.

Cursor on the model. Observe the panel.

Only the surface of the model is clipped.

Click on Use slab mode with thickness.


Type 0.5 in the text box and press enter.

Click on Use slab mode with thickness.

It allows you to view the portion of the model according to slab thickness. Change the slab thickness to 0.5. Type 0.5 in the text box and press enter. Observe the panel.

Click on enable mouse buttons for flipping plane,

change thickness, click on Adjust clipping with mouse.

Select button 2 for Translation.

Select button 3 for Rotation.

In the dialog-box, click on Adjust clipping with mouse.


Assign button 2 for Translation and Button 3 for rotation.

Click on Surface capping button.


Click on Cap surfaces at clip planes.

Click Use cap color.

Click on Surface capping button.

In the Surface capping dialog-box, select Cap surfaces at clip planes.

Click on Use cap color.

Click on color well. Click on the color well.


Select a color from the color-editor.

Click on solid radio button.


Click on Close.

Select solid as cap style.

Close the dialog-box.

Click on Actions>>Surface>>Transparency>>20%. On the Chimera window;

make the surface transparent upto 20% using Actions menu.

Cursor on the panel. Observe the panel.

The slab is now colored and transparent.

Press and hold the center mouse button.

Drag the mouse.

Press and hold the center mouse button.

Drag the mouse to move the clipping plane in one direction.

Hold the right mouse button and drag the mouse. To shift the clipping plane;

Hold the right mouse button and drag the mouse.

Cursor on the panel. Observe the panel,


Pocket holding the heme group is now visible very clearly.

Slide Number 7

Summary

Lets Summarize,

In this tutorial we have learnt to,

Show Axes, Planes and Centroids.

Show 2D Labels.

Draw Arrows.

Clip the model using Per-Model clipping tool

Slide Number 8

Assignment

Chymotrypsin (pdb code : 7GCH)

For the assignment,

Open a model of Chymotrypsin.

Draw planes.

Clip the structure using Per-Model Clipping tool.

Slide Number 9

Acknowledgement

This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.

Slide Number 10 We conduct workshops using Spoken Tutorials and give certificates.

Please contact us.

Slide number 11 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
This is Snehalatha from IIT Bombay signing off.

Thank you for joining.

Contributors and Content Editors

Snehalathak

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