Sandhya.np14 at 13:00, 28 June 2018

2018-06-28T13:00:33Z

PoojaMoolya: Created page with "{| border = 1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on Axes and Planes using Chimera. |- | 00:06 | In this tutorial, w..."

2018-01-15T12:04:48Z

Created page with "{| border = 1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on Axes and Planes using Chimera. |- | 00:06 | In this tutorial, w..."

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{| border = 1
! <center>Time</center>
! <center>Narration</center>

|-
| 00:01
| Welcome to this tutorial on Axes and Planes using Chimera.

|-
| 00:06
| In this tutorial, we will learn to show, '''Axes''', '''Planes''' and '''Centroids'''

|-
| 00:12
| '''2D Labels''' and '''Per-Model clipping'''.

|-
| 00:17
| To follow this tutorial you should be familiar with, '''Chimera''' Interface.

|-
| 00:23
| If not, for relevant tutorials, please visit our website.

|-
| 00:28
| To record this tutorial, I am using, '''Ubuntu''' OS version. 14.04

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| 00:34
| '''Chimera''' version 1.10.1

|-
| 00:38
| '''Mozilla firefox''' browser 42.0, and working Internet connection.

|-
| 00:45
| Here I have opened '''Chimera''' window.

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| 00:48
| On the command text box type, '''open 1EMA '''. Press enter

|-
| 00:55
| Structure of '''green fluorescent protein '''opens on the panel.

|-
| 01:00
| Click on the ''' Tools''' menu.

|-
| 01:02
| Scroll down to '''Structure Analysis''' option. From the sub-menu click on '''Axes, Planes, Centroids'''.

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| 01:11
| '''Structure Measurements''' dialog box opens.

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| 01:15
| Here we have '''Define axes, Define plane, Define centroid tabs'''.

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| 01:24
| Click on '''Define axes''' tab. This opens '''Define axes''' dialog box.

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| 01:31
| Here we can specify atom sets and other axis parameters.

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| 01:37
| On the panel, select a few residues of your choice, from the middle of the structure.

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| 01:43
| To select residues; Click on residues while pressing '''CTRL''' and '''shift''' keys simultaneously.

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| 01:55
| On the '''Define Axes '''dialog box, click on the radio button “'''Selected atoms'''”

|-
| 02:02
| Type the name of the axis as '''axis1.'''

|-
|02:06
| Click on the '''color well'''. Select a color from the '''color editor'''.

Close the '''color editor'''.

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| 02:14
| To change the thickness of the axis; click on '''angstroms''' radio button.

|-
| 02:19
| Change the number in the text box to 0.25

Click on '''OK''' button.

|-
| 02:27
| Observe the panel. '''Axis''' is drawn for the selected atoms.

|-
| 02:33
| Clear the selection using select menu.

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| 02:37
| An object for this axis is generated in the '''Structure Measurement''' dialog box.

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| 02:43
| To delete axis, click on the row. Click on '''Delete''' button at the bottom of the dialog-box.

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| 02:51
| Now to add '''plane''' to the structure, click on '''Define plane''' '''tab.'''

|-
| 02:57
| In the '''Define Plane''' dialog-box, change the name of the plane to '''plane1'''.

|-
| 03:03
| Here a '''plane''' is created only for selected atoms.

|-
| 03:08
| On the panel, Select few residues of your choice, from the middle of the structure.

|-
| 03:14
| Press '''CTRL''' and '''Shift''' keys simultaneously and click on the residues.

|-
| 03:23
| On the '''Define Plane''' dialog-box; Click on the '''color well.'''

|-
| 03:28
| Choose a color from the '''color editor'''. Close the '''color-editor.'''

|-
| 03:34
| Click on''' OK''' button. Observe the panel.

|-
| 03:39
| A '''plane '''is generated based on the selected atoms.

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| 03:44
| Clear the selection using '''Select''' menu.

|-
| 03:48
| Delete the '''plane''', click on the plane ID in the '''Structure Measurements''' dialog box.

|-
| 03:55
| Click on delete button.

|-
| 03:58
| To show '''centroid''', click on '''Define centroid''' '''tab.'''

|-
| 04:03
| '''Define centroid''' dialog box opens.

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| 04:07
| Select residues 64 and 68 on the structure to create a centroid.

|-
| 04:14
| In the '''Define Centroid''' dialog box; type the name of the centroid as '''centroid1'''.

|-
| 04:21
| As shown earlier, select a color from the color well.

|-
| 04:26
| Close the '''color-editor'''. Click on '''OK''' button.

|-
| 04:31
| '''Centroid''' for the chosen atoms is displayed on the panel.

|-
| 04:36
| Clear the selection and delete the '''centroid'''.

|-
| 04:42
| Close the '''Structure Measurements''' dialog box.

|-
| 04:45
| '''2D-Labels''' such text and arrows can also be added to the structure.

|-
| 04:52
| Start '''2D labels''' tool using''' Utilities''' option from the '''Tools''' menu.

|-
| 04:59
| '''2D-Labels '''dialog-box opens with tabs for '''Labels''', '''Arrows''' and '''color key'''.

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| 05:07
| Click on '''Labels''' tab to add labels.

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| 05:11
| By default '''use mouse for label placement''' option near the bottom of the dialog box is selected.

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| 05:20
| Click on the '''color well''', select a color for the label. Close the '''color editor'''.

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| 05:28
| Click on the panel where you want to place the label.

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| 05:32
| Label id with X and Y coordinates appears on the dialog-box.

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| 05:38
| Now type the label text in the '''Text''' area.

|-
| 05:42
| Type '''Green Fluorescent Protein'''. Press enter.

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| 05:49
| The label created can be repositioned by dragging using left mouse button.

|-
| 05:56
| To delete the label, select the label id on the dialog-box.

Click on '''delete''' button.

|-
| 06:05
| Click on '''Arrows tab''' in the dialog-box to add arrows.

|-
| 06:10
| In the '''Arrow weight''' field at the bottom of the dialog-box;

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| 06:15
| Change the number to change the thickness of the arrow.

|-
| 06:19
| I will type 0.5 to create a thinner arrow.

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| 06:24
| Click on the '''Arrow head''' style button. Choose an option from the drop-down menu.

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| 06:30
| I will choose '''Pointy'''.

|-
| 06:33
| Place the cursor on the panel, click and hold the mouse button.

|-
| 06:39
| Drag to extend the arrow. Release the mouse button.

|-
| 06:46
| Drag the end of the arrow to reorient or to change its length.

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| 06:54
| Move the arrow by dragging it from the middle.

|-
| 06:58
| Change the color of the arrow by clicking on the color well next to the arrow id.

|-
| 07:04
| Select a color. Close the '''color-editor'''.

|-
| 07:08
| Close the '''2D-Labels '''dialog-box. Close the session using '''File''' menu.

|-
| 07:15
| Open a new session.

|-
| 07:18
| To demonstrate '''per-model clipping;''' I will use structure of '''myoglobin''' as an example.

|-
| 07:25
| On the command text box type '''open 1mbo'''. Press enter.

|-
| 07:32
| Scroll down the '''Tools''' menu, select '''Depiction'''.

|-
| 07:37
| From the sub-menu, click on '''Per-Model clipping'''.

|-
| 07:42
| '''Per-Model clipping''' dialog-box opens.

|-
| 07:46
| '''Per-Model Clipping''' allows different models to be clipped in different ways.

|-
| 07:52
| It is a single plane that separates the visible and invisible portions of the model.

|-
| 07:59
| Each model can have only one '''Per-Model Clipping''' plane.

|-
| 08:04
| A model and its surface are treated as separate models.

|-
| 08:09
| Back to the panel. Model drop-down menu in the '''Per-Model Clipping''' dialog-box shows the current model.

|-
| 08:18
| Select '''Enable clipping''', this activates the clipping planes.

|-
| 08:25
| Visible portion of the model is behind the plane. Uncheck '''Enable clipping.'''

|-
| 08:33
| Create a surface for the model. Click on''' Actions''' menu, scroll down to '''Surface'''.

Click on '''Show'''.

|-
| 08:43
| Now the structure shows a pocket where '''Heme''' group is bound tightly.

|-
| 08:50
| In the''' dialog-box, Model''' drop-down menu, shows two models.

Model (1mbo) and Model with surface.

|-
| 09:00
| Select model with surface. Click on '''Enable clipping'''.

|-
| 09:06
| Observe the panel.

|-
| 09:10
| Only the surface of the model is clipped.

|-
| 09:14
| Click on '''Use slab mode with thickness'''.

|-
| 09:18
| It allows you to view the portion of the model according to slab thickness.

|-
| 09:24
| Change the slab thickness to 0.5.

|-
| 09:28
| Type 0.5 in the text box and press enter. Observe the panel.

|-
| 09:37
| In the dialog-box, click on '''Adjust clipping with mouse'''.

|-
| 09:43
| Assign button 2 for Translation and Button 3 for rotation.

|-
| 09:51
| Click on '''Surface capping''' button.

|-
| 09:55
| In the '''Surface capping''' dialog-box, select '''Cap surfaces at clip planes'''.

|-
| 10:02
| Click on '''Use cap color'''.

|-
| 10:05
| Select a color from the '''color well'''.

|-
| 10:09
| Close the '''color editor'''. Select '''solid''' as cap style.

Close the '''dialog-box'''.

|-
|10:18
| On the Chimera window, make the surface transparent upto 20% using '''Actions''' menu.

|-
| 10:26
| Observe the panel. The slab is now colored and transparent.

|-
| 10:33
| Press and hold the center mouse button. Drag the mouse to move the clipping plane in one direction.

|-
| 10:42
| To shift the clipping plane, Hold the right mouse button and drag the mouse.

|-
| 10:50
| Observe the panel, Pocket holding the heme group is now visible very clearly.

|-
| 10:57
| Lets Summarize, In this tutorial we have learnt to,

Show Axes, Planes and Centroids.

|-
| 11:05
| Show 2D Labels.

Draw Arrows.

|-
|11:09
|Clip the model using '''Per-Model''' clipping tool

|-
| 11:13
| For the assignment, Open a model of '''Chymotrypsin'''.

|-
| 11:18
|Draw planes. Clip the structure using''' Per-Model Clipping''' tool.

|-
| 11:24
| This video summarizes the Spoken Tutorial project.
If you do not have good bandwidth, you can download and watch it.

|-
| 11:32
| We conduct workshops using Spoken Tutorials and give certificates.
Please contact us.

|-
| 11:39
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.

|-
| 11:45
| This is Snehalatha from IIT Bombay signing off.

Thank you for joining.

|}

UCSF-Chimera/C4/Axes-and-Planes/English-timed - Revision history

Sandhya.np14 at 13:00, 28 June 2018

PoojaMoolya: Created page with "{| border = 1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on Axes and Planes using Chimera. |- | 00:06 | In this tutorial, w..."