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