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

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 as 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 up to 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