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

From Script | Spoken-Tutorial
Jump to: navigation, search
(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...")
 
 
Line 5: Line 5:
 
|-
 
|-
 
| 00:01
 
| 00:01
−
|  Welcome to this tutorial on Axes and Planes using Chimera.
+
|  Welcome to this tutorial on '''Axes and Planes''' using '''Chimera'''.
  
 
|-
 
|-
 
| 00:06
 
| 00:06
−
|  In this tutorial, we will learn to show, '''Axes''', '''Planes''' and '''Centroids'''
+
|  In this tutorial, we will learn to show '''Axes, Planes''' and '''Centroids''',
  
 
|-
 
|-
Line 17: Line 17:
 
|-
 
|-
 
| 00:17
 
| 00:17
−
|  To follow this tutorial you should be familiar with, '''Chimera''' Interface.
+
|  To follow this tutorial, you should be familiar with '''Chimera''' interface.
  
 
|-
 
|-
 
| 00:23
 
| 00:23
−
| If not, for relevant tutorials, please visit our website.  
+
| If not, for relevant tutorials, please visit our '''website'''.  
  
 
|-
 
|-
 
| 00:28
 
| 00:28
−
|  To record this tutorial, I am using, '''Ubuntu''' OS version. 14.04
+
|  To record this tutorial, I am using: '''Ubuntu OS''' version '''14.04''',
  
 
|-
 
|-
 
| 00:34
 
| 00:34
−
| '''Chimera''' version 1.10.1
+
| '''Chimera''' version '''1.10.1''',
  
 
|-
 
|-
 
| 00:38
 
| 00:38
−
| '''Mozilla firefox''' browser 42.0, and  working Internet connection.
+
| '''Mozilla firefox''' browser '''42.0''' and  working '''internet''' connection.
  
 
|-
 
|-
 
| 00:45
 
| 00:45
−
|  Here I have opened '''Chimera''' window.
+
|  Here, I have opened '''Chimera''' window.
  
 
|-
 
|-
 
| 00:48
 
| 00:48
−
|  On the command text box type,  '''open 1EMA '''. Press enter
+
|  On the '''command''' text box, type: '''open 1EMA '''. Press '''Enter'''.
  
 
|-
 
|-
 
| 00:55
 
| 00:55
−
|  Structure of '''green fluorescent protein '''opens on the panel.
+
|  Structure of green fluorescent protein opens on the panel.
  
 
|-
 
|-
Line 53: Line 53:
 
|-
 
|-
 
| 01:02
 
| 01:02
−
|  Scroll down to '''Structure Analysis''' option.  From the sub-menu click on '''Axes, Planes, Centroids'''.
+
|  Scroll down to '''Structure Analysis''' option.  From the sub-menu, click on '''Axes, Planes, Centroids'''.
  
 
|-
 
|-
Line 73: Line 73:
 
|-
 
|-
 
| 01:37
 
| 01:37
−
|  On the panel, select a few residues of your choice, from the middle of the structure.
+
|  On the panel, select a few '''residues''' of your choice, from the middle of the structure.
  
 
|-
 
|-
 
| 01:43
 
| 01:43
−
|  To select residues; Click on residues while pressing '''CTRL''' and '''shift''' keys simultaneously.
+
|  To select residues- click on residues while pressing '''CTRL''' and '''shift''' keys simultaneously.
  
 
|-
 
|-
 
| 01:55
 
| 01:55
−
|  On the '''Define Axes '''dialog box, click on the radio button “'''Selected atoms'''”
+
|  On the '''Define Axes '''dialog box, click on the '''radio button''' “'''Selected atoms'''”.
  
 
|-
 
|-
Line 90: Line 90:
 
|02:06
 
|02:06
 
|  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'''.
 
Close the '''color editor'''.
  
 
|-
 
|-
 
| 02:14
 
| 02:14
−
|  To change the thickness of the axis; click on '''angstroms''' radio button.
+
|  To change the thickness of the axis- click on '''angstroms''' radio button.
  
 
|-
 
|-
 
| 02:19
 
| 02:19
−
|  Change the number in the text box to 0.25
+
|  Change the number in the text box to 0.25.
−
 
+
 
Click on '''OK''' button.
 
Click on '''OK''' button.
  
Line 109: Line 107:
 
|-
 
|-
 
| 02:33
 
| 02:33
−
|  Clear the selection using select menu.
+
|  Clear the selection using '''Select''' menu.
  
 
|-
 
|-
Line 121: Line 119:
 
|-
 
|-
 
| 02:51
 
| 02:51
−
|  Now to add '''plane''' to the structure, click on '''Define plane''' '''tab.'''
+
|  Now to add '''plane''' to the structure, click on '''Define plane''' tab.
  
 
|-
 
|-
Line 133: Line 131:
 
|-
 
|-
 
| 03:08
 
| 03:08
−
|  On the panel, Select few residues of your choice, from the middle of the structure.
+
|  On the panel, select few residues of your choice, from the middle of the structure.
  
 
|-
 
|-
Line 141: Line 139:
 
|-
 
|-
 
| 03:23
 
| 03:23
−
|  On the '''Define Plane''' dialog-box; Click on the '''color well.'''  
+
|  On the '''Define Plane''' dialog-box- Click on the '''color well.'''  
  
 
|-
 
|-
Line 161: Line 159:
 
|-
 
|-
 
| 03:48
 
| 03:48
−
|  Delete the '''plane''', click on the plane ID in the '''Structure Measurements''' dialog box.
+
|  Delete the '''plane''', click on the '''plane ID''' in the '''Structure Measurements''' dialog box.
  
 
|-
 
|-
 
| 03:55
 
| 03:55
−
| Click on delete button.
+
| Click on '''Delete''' button.
  
 
|-
 
|-
 
| 03:58
 
| 03:58
−
|  To show '''centroid''', click on '''Define centroid''' '''tab.'''
+
|  To show '''centroid''', click on '''Define centroid''' tab.
  
 
|-
 
|-
Line 177: Line 175:
 
|-
 
|-
 
| 04:07
 
| 04:07
−
|  Select residues 64 and 68 on the structure to create a centroid.
+
|  Select '''residues 64''' and '''68''' on the structure to create a centroid.
  
 
|-
 
|-
 
| 04:14
 
| 04:14
−
|  In the '''Define Centroid''' dialog box; type the name of the centroid as '''centroid1'''.
+
|  In the '''Define Centroid''' dialog box, type the name of the centroid as '''centroid1'''.
  
 
|-
 
|-
 
| 04:21
 
| 04:21
−
|  As shown earlier, select a color from the color well.
+
|  As shown earlier, select a color from the '''color well'''.
  
 
|-
 
|-
Line 193: Line 191:
 
|-
 
|-
 
| 04:31
 
| 04:31
−
|  '''Centroid''' for the chosen atoms is displayed on the panel.
+
|  '''Centroid''' for the chosen atoms is displayed on the '''panel'''.
  
 
|-
 
|-
Line 205: Line 203:
 
|-
 
|-
 
| 04:45
 
| 04:45
−
|  '''2D-Labels''' such text and arrows can also be added to the structure.  
+
|  '''2D-Labels''' such as text and arrows can also be added to the structure.  
  
 
|-
 
|-
 
| 04:52
 
| 04:52
−
|  Start '''2D labels''' tool using''' Utilities''' option from the '''Tools''' menu.
+
|  Start '''2D labels''' tool, using''' Utilities''' option from the '''Tools''' menu.
  
 
|-
 
|-
Line 221: Line 219:
 
|-
 
|-
 
| 05:11
 
| 05:11
−
| By default '''use mouse for label placement''' option near the bottom of the dialog box is selected.
+
| By default, '''use mouse for label placement''' option near the bottom of the dialog box is selected.
  
 
|-
 
|-
Line 233: Line 231:
 
|-
 
|-
 
| 05:32
 
| 05:32
−
|  Label id with X and Y coordinates appears on the dialog-box.
+
|  '''Label id''' with X and Y coordinates appears on the dialog-box.
  
 
|-
 
|-
 
| 05:38
 
| 05:38
−
|  Now type the label text in the '''Text''' area.
+
|  Now, type the label text in the '''Text''' area.
  
 
|-
 
|-
 
| 05:42
 
| 05:42
−
| Type '''Green Fluorescent Protein'''.  Press enter.
+
| Type '''Green Fluorescent Protein'''.  Press '''Enter'''.
  
 
|-
 
|-
 
| 05:49
 
| 05:49
−
|  The label created can be repositioned by dragging using left mouse button.
+
|  The label created can be repositioned by dragging using left '''mouse button'''.
  
 
|-
 
|-
 
| 05:56
 
| 05:56
−
|  To delete the label, select the label id on the dialog-box.
+
|  To delete the label, select the '''label id''' on the dialog-box.
−
 
+
 
Click on '''delete''' button.
 
Click on '''delete''' button.
  
 
|-
 
|-
 
| 06:05
 
| 06:05
−
|  Click on '''Arrows tab''' in the dialog-box to add arrows.
+
|  Click on '''Arrows''' tab in the dialog-box to add arrows.
  
 
|-
 
|-
 
| 06:10
 
| 06:10
−
|  In the '''Arrow weight''' field at the bottom of the dialog-box;
+
|  In the '''Arrow weight''' field at the bottom of the dialog-box,
  
 
|-
 
|-
 
| 06:15
 
| 06:15
−
| Change the number to change the thickness of the arrow.
+
| change the number to change the thickness of the arrow.
  
 
|-
 
|-
 
| 06:19
 
| 06:19
−
| I will type 0.5 to create a thinner arrow.
+
| I will type '''0.5''' to create a thinner arrow.
  
 
|-
 
|-
 
| 06:24
 
| 06:24
−
| Click on the '''Arrow head''' style button. Choose an option from the drop-down menu.
+
| Click on the '''Arrow head style''' button. Choose an option from the drop-down menu.
  
 
|-
 
|-
Line 279: Line 276:
 
|-
 
|-
 
| 06:33
 
| 06:33
−
|  Place the cursor on the panel, click and hold the mouse button.  
+
|  Place the cursor on the panel, click and hold the '''mouse''' button.  
  
 
|-
 
|-
Line 295: Line 292:
 
|-
 
|-
 
| 06:58
 
| 06:58
−
|  Change the color of the arrow by clicking on the color well next to the arrow id.
+
|  Change the color of the arrow by clicking on the '''color well''' next to the '''arrow id'''.
  
 
|-
 
|-
Line 311: Line 308:
 
|-
 
|-
 
| 07:18
 
| 07:18
−
|  To demonstrate '''per-model clipping;'''  I will use structure of '''myoglobin''' as an example.
+
|  To demonstrate '''per-model clipping-'''  I will use structure of '''myoglobin''' as an example.
  
 
|-
 
|-
 
| 07:25
 
| 07:25
−
| On the command text box type '''open 1mbo'''.  Press enter.
+
| On the '''command''' text box, type '''open 1mbo'''.  Press '''Enter'''.
  
 
|-
 
|-
Line 347: Line 344:
 
|-
 
|-
 
| 08:09
 
| 08:09
−
|  Back to the panel. Model drop-down menu in the '''Per-Model Clipping''' dialog-box shows the current model.
+
|  Back to the panel. '''Model''' drop-down menu in the '''Per-Model Clipping''' dialog-box shows the current model.
  
 
|-
 
|-
 
| 08:18
 
| 08:18
−
|  Select '''Enable clipping''', this activates the clipping planes.
+
|  Select '''Enable clipping'''; this activates the clipping planes.
  
 
|-
 
|-
Line 360: Line 357:
 
| 08:33
 
| 08:33
 
|  Create a surface for the model.  Click on''' Actions''' menu, scroll down to '''Surface'''.  
 
|  Create a surface for the model.  Click on''' Actions''' menu, scroll down to '''Surface'''.  
−
 
 
Click on '''Show'''.
 
Click on '''Show'''.
  
Line 369: Line 365:
 
|-
 
|-
 
| 08:50
 
| 08:50
−
|  In the''' dialog-box, Model''' drop-down menu, shows two models.
+
|  In the dialog-box '''Model''' drop-down menu, shows two models.
−
 
+
'''Model (1mbo)''' and  Model with surface.  
−
Model (1mbo) and  Model with surface.  
+
  
 
|-
 
|-
Line 395: Line 390:
 
|-
 
|-
 
| 09:24
 
| 09:24
−
| Change the slab thickness to 0.5.
+
| Change the slab thickness to '''0.5'''.
  
 
|-
 
|-
 
| 09:28
 
| 09:28
−
| Type 0.5 in the text box and press enter. Observe the panel.
+
| Type '''0.5''' in the text box and press '''Enter'''. Observe the panel.
  
 
|-
 
|-
Line 407: Line 402:
 
|-
 
|-
 
| 09:43
 
| 09:43
−
| Assign button 2 for Translation and Button 3 for rotation.  
+
| Assign '''button 2''' for '''Translation''' and '''button 3''' for '''Rotation'''.  
  
 
|-
 
|-
Line 428: Line 423:
 
| 10:09
 
| 10:09
 
| Close the '''color editor'''. Select '''solid''' as cap style.
 
| Close the '''color editor'''. Select '''solid''' as cap style.
−
 
 
Close the '''dialog-box'''.
 
Close the '''dialog-box'''.
  
 
|-
 
|-
 
|10:18
 
|10:18
−
|  On the Chimera window, make the surface transparent upto 20% using '''Actions''' menu.
+
|  On the '''Chimera''' window, make the surface transparent up to 20% using '''Actions''' menu.
  
 
|-
 
|-
 
| 10:26
 
| 10:26
−
|  Observe the panel. The slab is now colored and transparent.
+
|  Observe the panel. The '''slab''' is now colored and transparent.
  
 
|-
 
|-
 
| 10:33
 
| 10:33
−
|  Press and hold the center mouse button. Drag the mouse to move the clipping plane in one direction.
+
|  Press and hold the center mouse button. Drag the '''mouse''' to move the clipping plane in one direction.
  
 
|-
 
|-
 
| 10:42
 
| 10:42
−
|  To shift the clipping plane, Hold the right mouse button and drag the mouse.
+
|  To shift the clipping plane, hold the right mouse button and drag the '''mouse'''.
  
 
|-
 
|-
 
| 10:50
 
| 10:50
−
|  Observe the panel, Pocket holding the heme group is now visible very clearly.
+
|  Observe the panel. Pocket holding the '''heme''' group is now visible very clearly.
  
 
|-
 
|-
 
| 10:57
 
| 10:57
−
|  Lets Summarize, In this tutorial we have learnt to,
+
|  Lets Summarize, In this tutorial, we have learnt to- show '''Axes, Planes''' and '''Centroids''',
−
 
+
−
Show Axes, Planes and Centroids.
+
  
 
|-
 
|-
 
| 11:05
 
| 11:05
−
| Show 2D Labels.
+
| show '''2D Label'''s,
−
 
+
Draw Arrows,
−
Draw Arrows.
+
  
 
|-
 
|-
 
|11:09
 
|11:09
−
|Clip the model using '''Per-Model''' clipping tool
+
|Clip the model using '''Per-Model''' clipping tool.
  
 
|-
 
|-
 
| 11:13
 
| 11:13
−
|  For the assignment, Open a model of '''Chymotrypsin'''.
+
|  For the assignment, open a model of '''Chymotrypsin'''.
  
 
|-
 
|-
Line 477: Line 468:
 
|-
 
|-
 
| 11:24
 
| 11:24
−
| This video summarizes the Spoken Tutorial project.
+
| This video summarizes the '''Spoken Tutorial''' project. If you do not have good '''bandwidth''', you can download and watch it.
−
If you do not have good bandwidth, you can download and watch it.
+
  
 
|-
 
|-
Line 487: Line 477:
 
|-
 
|-
 
| 11:39
 
| 11:39
−
|  The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.  
+
|  The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.  
  
 
|-
 
|-
 
| 11:45
 
| 11:45
−
|  This is Snehalatha from IIT Bombay signing off.  
+
|  This is Snehalatha from IIT Bombay, signing off.  
−
 
+
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 18:30, 28 June 2018

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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C4/Axes-and-Planes/English-timed&oldid=43581"