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

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Time
Narration
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
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.
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.
01:11 Structure Measurements dialog box opens.
01:15 Here we have Define axes, Define plane, Define centroid tabs.
01:24 Click on Define axes tab. This opens Define axes dialog box.
01:31 Here we can specify atom sets and other axis parameters.
01:37 On the panel, select a few residues of your choice, from the middle of the structure.
01:43 To select residues; Click on residues while pressing CTRL and shift keys simultaneously.
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.

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.
02:37 An object for this axis is generated in the Structure Measurement dialog box.
02:43 To delete axis, click on the row. Click on Delete button at the bottom of the dialog-box.
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.
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.
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.
05:07 Click on Labels tab to add labels.
05:11 By default use mouse for label placement option near the bottom of the dialog box is selected.
05:20 Click on the color well, select a color for the label. Close the color editor.
05:28 Click on the panel where you want to place the label.
05:32 Label id with X and Y coordinates appears on the dialog-box.
05:38 Now type the label text in the Text area.
05:42 Type Green Fluorescent Protein. Press enter.
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;
06:15 Change the number to change the thickness of the arrow.
06:19 I will type 0.5 to create a thinner arrow.
06:24 Click on the Arrow head style button. Choose an option from the drop-down menu.
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.
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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14