Difference between revisions of "UCSF-Chimera/C4/Attributes/English"
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'''Title Slide''' | '''Title Slide''' | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Attributes.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Attributes.''' | ||
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'''Learning Objectives''' | '''Learning Objectives''' | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we will learn to, | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we will learn to, | ||
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* Change '''attributes''' of atoms, residues and models. | * Change '''attributes''' of atoms, residues and models. | ||
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* Color atoms in a protein according to '''B-factor''' values. | * Color atoms in a protein according to '''B-factor''' values. | ||
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* Color residues according to '''kdhydrophobicity''' values. | * Color residues according to '''kdhydrophobicity''' values. | ||
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'''Pre-requisites''' | '''Pre-requisites''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with '''Chimera''' interface |
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| − | '''Chimera''' interface | + | |
If not, for relevant tutorials, please visit our website. | If not, for relevant tutorials, please visit our website. | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using | ||
| − | '''Ubuntu''' OS version. 14.04 | + | *'''Ubuntu''' OS version. 14.04 |
| − | + | *'''Chimera''' version 1.10.2 | |
| − | '''Chimera''' version 1.10.2 | + | *'''Mozilla Firefox''' browser 42.0 |
| − | + | *And a working Internet connection. | |
| − | '''Mozilla Firefox''' browser 42.0 | + | |
| − | + | ||
| − | And a working Internet connection. | + | |
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| − | Type, '''open | + | Type, '''open 1zik''' |
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| − | On the command text box, type, '''open | + | On the command text box, type, '''open 1zik''' |
| − | Press | + | Press '''Enter'''. |
|- | |- | ||
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| − | Press | + | Press '''Enter'''. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide water molecules, on the '''command line''' type, | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide water molecules, on the '''command line''' type, | ||
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| − | Press | + | Press '''Enter'''. |
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| − | Press | + | Press '''Enter'''. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the display to sticks, type, | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the display to sticks, type, | ||
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'''rep stick''' | '''rep stick''' | ||
| − | Press | + | Press '''Enter'''. |
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* '''Attributes ''' are properties with names and values. | * '''Attributes ''' are properties with names and values. | ||
| − | + | * In '''Chimera''', items such as '''atoms, bonds, residues''' and '''molecule models''' have '''Attributes.''' | |
| − | * In Chimera, items such as atoms, bonds, residues and molecule models have '''Attributes.''' | + | |
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| − | Click on | + | Click on “'''attributes'''” button on the right side of the panel. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Model Panel''' dialog box appears on the screen. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Model Panel''' dialog box appears on the screen. | ||
Click on the '''attributes''' button on the right side of the panel. | Click on the '''attributes''' button on the right side of the panel. | ||
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| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''1zik | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''1zik Attributes''' dialog box. |
Click on '''Molecule Attributes''' button. | Click on '''Molecule Attributes''' button. | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|'''Attributes''' dialog box for '''1zik''' opens on the screen. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|'''Attributes''' dialog box for '''1zik''' opens on the screen. | ||
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The dialog box has '''attribute''' list. | The dialog box has '''attribute''' list. | ||
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Select '''True''' from the drop-down menu. | Select '''True''' from the drop-down menu. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For example | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For example - |
| − | + | ||
| − | + | To change the display of aromatic rings, click on the button next to '''aromatic display'''. | |
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel. | ||
| − | All the aromatic rings are shown with disks in the center. | + | All the '''aromatic rings''' are shown with disks in the center. |
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'''rep bs''' | '''rep bs''' | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Change the '''ball scale '''value to '''0.5'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Change the '''ball scale '''value to '''0.5'''. | ||
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Change the value of '''ball scale''' to 0.5. | Change the value of '''ball scale''' to 0.5. | ||
| − | + | Press '''Enter'''. | |
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| − | + | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again click on '''Molecular Attributes '''check box. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again click on '''Molecular Attributes '''check box. | ||
| − | From the list, click on '''Component | + | From the list, click on '''Component Atom Attributes'''. |
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Observe the panel. | Observe the panel. | ||
| − | Select '''dot''' to bring back the sticks display. | + | Select '''dot''' to bring back the '''sticks''' display. |
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Here we have options to change the attributes of the ribbon. | Here we have options to change the attributes of the ribbon. | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Presets menu, change the display to''' ribbons'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Presets menu, change the display to''' ribbons'''. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Using presets menu, change the display of the structure on the panel to '''ribbons'''. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Using '''presets''' menu, change the display of the structure on the panel to '''ribbons'''. |
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, click in the '''Attribute '''dialog box, | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, click in the '''Attribute '''dialog box, | ||
| − | Now,in the | + | Now,in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''. |
| − | + | ||
| − | + | ||
| − | + | ||
| + | Select a ribbon color. | ||
| + | And click on '''close''' option to close the '''color editor'''. | ||
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|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Presets''' menu, select '''Interactive 2 '''option. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Presets''' menu, select '''Interactive 2 '''option. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again change the display to '''atoms '''using '''Presets '''menu. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again, change the display to '''atoms '''using '''Presets '''menu. |
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From the sub-menu select '''Render by Attribute.''' | From the sub-menu select '''Render by Attribute.''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Tools''' menu, scroll down to '''Structure Analysis'''. |
And select '''Render by Attribute '''option from the sub-menu. | And select '''Render by Attribute '''option from the sub-menu. | ||
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|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the dialog box. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the dialog box. | ||
| − | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Render by attribute''' dialog box opens. | |
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| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | + | |
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Click on '''atoms''' from the '''Attributes''' drop-down. | Click on '''atoms''' from the '''Attributes''' drop-down. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here we have options to change the '''attributes '''of '''atoms, | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here we have options to change the '''attributes '''of '''atoms, residues, molecules, segmentation regions''' etc. |
Select '''atoms.''' | Select '''atoms.''' | ||
| − | + | Click on''' Render.''' | |
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| − | The list shows two options | + | The list shows two options: '''bfactor''' and '''occupancy''' |
| − | + | ||
| − | + | ||
| − | '''bfactor''' and '''occupancy''' | + | |
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | ||
| − | * '''B-factor''' values are a measure of mobility in the macromolecule. | + | * '''B-factor''' values are a measure of mobility in the '''macromolecule'''. |
| − | * Atoms with low '''B-factor''' values belong to a part of the structure that is well ordered. | + | * '''Atoms''' with low '''B-factor''' values belong to a part of the structure that is well ordered. |
* Atoms with large '''B-factor''' values belong to part of the structure that is very flexible. | * Atoms with large '''B-factor''' values belong to part of the structure that is very flexible. | ||
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'''B-factor''' | '''B-factor''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| PDB file for a protein structure contains B-factor information. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| PDB file for a '''protein''' structure contains B-factor information. |
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The vertical bars can be dragged along the '''histogram''' with the mouse. | The vertical bars can be dragged along the '''histogram''' with the mouse. | ||
| − | The | + | The value of B-factor is displayed in the ''' Value ''' text box. |
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| − | Click on ''' | + | Click on '''Colors''' button. |
Click on '''color atoms, keep opaque '''and''' color surfaces.''' | Click on '''color atoms, keep opaque '''and''' color surfaces.''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|Check options for '''color atoms''', '''keep opaque''' and '''color surfaces.''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|Click on '''Colors''' button. |
| + | |||
| + | Check options for '''color atoms''', '''keep opaque''' and '''color surfaces.''' | ||
The default color '''palette''' is blue and red. | The default color '''palette''' is blue and red. | ||
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|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | |||
| − | |||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel. | ||
| − | Atoms with high '''B-factor''' values are shown in red and least in blue. | + | '''Atoms''' with high '''B-factor''' values are shown in red and least in blue. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As expected atoms with high '''B-factors''' are on the outside of the structure. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As expected, '''atoms''' with high '''B-factors''' are on the outside of the structure. |
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select '''residues '''in the''' attributes drop-down''' in the''' Render dialog box.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select '''residues '''in the''' attributes drop-down''' in the''' Render dialog box.''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the '''Select by Attribute | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the '''Select by Attribute''' dialog box, click on '''Attributes button.''' |
From the drop-down, select '''residues'''. | From the drop-down, select '''residues'''. | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Render.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Render.''' | ||
| − | The '''attributes''' for residues include '''kdHydrophobicity scale'''. | + | The '''attributes''' for '''residues''' include '''kdHydrophobicity scale'''. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''kdHydrophobicity ''' from the drop-down menu. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''kdHydrophobicity ''' from the drop-down menu. | ||
| − | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''kdHydrophobicity''' from the drop-down menu. | |
| − | + | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''kdHydrophobicity from the drop-down menu. | + | |
| − | + | ||
The values are displayed in the histogram. | The values are displayed in the histogram. | ||
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'''kdHydrophobicity ''' | '''kdHydrophobicity ''' | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | ||
| − | * '''kdHydrophobicity scales''' are values that define relative '''hydrophobicity''' of amino acid residues. | + | * '''kdHydrophobicity scales''' are values that define relative '''hydrophobicity''' of '''amino acid residues'''. |
| − | + | * '''KdHydrophobicity''' values are positive for '''hydrophobic residues''' and Negative values for '''polar residues'''. | |
| − | + | ||
| − | * '''KdHydrophobicity''' values are positive for '''hydrophobic''' | + | |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Hydrophobicity''' of the residues can be shown with colors or worms. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Hydrophobicity''' of the '''residues''' can be shown with colors or worms. |
| − | Choose '''Colors'''. By default some of the parameters are selected. | + | Choose '''Colors'''. By default, some of the parameters are selected. |
| − | Click on '''Apply''' button. | + | Click on '''Apply''' button. Observe the panel. |
| − | The '''hydrophobic''' | + | The '''hydrophobic residues''' are colored in red, and '''polar residues''' are colored in blue. |
|- | |- | ||
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Click on '''apply'''. | Click on '''apply'''. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Worms''' button | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Worms''' button. Click on '''Apply'''. |
Observe the panel. | Observe the panel. | ||
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Most '''hydrophobic residues''' face the interior of the structure. | |
| − | + | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Most '''hydrophobic''' | + | |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default, the more '''hydrophobic''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default, the more '''hydrophobic residues''' will be shown with larger radius. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''worm style''' to '''non-worm'''. Click on '''OK'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''worm style''' to '''non-worm'''. Click on '''OK'''. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To return the structure to normal '''ribbon''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To return the structure to normal '''ribbon''': |
| − | Click on worm-style button and choose '''non-worm''' option. Click on '''OK '''button | + | *Click on worm-style button and choose '''non-worm''' option. |
| + | *Click on '''OK '''button. | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''File''' menu, scroll down and click on '''Close Session''' option. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''File''' menu, scroll down and click on '''Close Session''' option. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Close the '''Chimera''' session using '''File''' menu. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Close the '''Chimera''' session using '''File''' menu. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 546: | Line 488: | ||
In this tutorial we have learnt to, | In this tutorial we have learnt to, | ||
| − | |||
| − | |||
* Change '''attributes''' of '''atoms, residues '''and''' models.''' | * Change '''attributes''' of '''atoms, residues '''and''' models.''' | ||
| − | + | * Color '''atoms''' in a '''protein''' according to '''B-factor''' values. | |
| − | + | * Color '''residues''' according to '''kdHydrophobicity '''values. | |
| − | * Color atoms in a protein according to '''B-factor''' values. | + | |
| − | + | ||
| − | + | ||
| − | * Color residues according to '''kdHydrophobicity '''values. | + | |
| − | + | ||
| − | + | ||
| − | + | ||
|- | |- | ||
| Line 564: | Line 497: | ||
Assignment | Assignment | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As an '''Assignment,''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As an '''Assignment,''' | ||
| − | |||
| − | |||
* Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. | * Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. | ||
| − | |||
| − | |||
* Color the atoms according to '''B-factor''' values. | * Color the atoms according to '''B-factor''' values. | ||
| − | |||
| − | |||
* Color the residues according to '''kdHydrophobicity '''values. | * Color the residues according to '''kdHydrophobicity '''values. | ||
| Line 580: | Line 507: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * This video summarizes the Spoken Tutorial project | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * 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. | ||
| − | |||
| − | |||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * We conduct workshops using Spoken Tutorials and give certificates. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| |
| + | * We conduct workshops using Spoken Tutorials and give certificates. | ||
* Please contact us. | * Please contact us. | ||
| − | |||
| − | |||
|- | |- | ||
Latest revision as of 08:08, 9 September 2016
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|---|---|
| Slide Number 1
Title Slide |
Welcome to this tutorial on Attributes. |
| Slide Number 2
Learning Objectives |
In this tutorial we will learn to,
|
| Slide Number 3
Pre-requisites |
To follow this tutorial you should be familiar with Chimera interface
If not, for relevant tutorials, please visit our website. |
| Slide Number 4
System Requirement |
To record this tutorial I am using
|
| Double-click on the Chimera icon present on the desk top.
|
Here I have opened a Chimera window.
|
| Cursor on the panel.
|
The model on the panel is shown as ribbons.
|
| On the command line type,
delete solvent.
|
To hide water molecules, on the command line type,
delete solvent.
|
| On the command line type,
rep sticks
|
To change the display to sticks, type,
Press Enter. |
| On the command line type,
|
Add hydrogens to the structure, type,
addh |
| Cursor on the panel. | Now let us learn how to change the attributes of atoms and residues for this structure. |
| Slide Number 5
Attributes |
|
| Cursor on the panel. | There are different ways to change the Attributes. |
| Click on the Favorites menu, scroll down and click on Model Panel. | Open the Model Panel using Favorites menu. |
| Cursor on the Model Panel dialog box.
|
Model Panel dialog box appears on the screen.
|
| Cursor on the 1zik Attributes dialog box.
Click on Molecule Attributes button. |
Attributes dialog box for 1zik opens on the screen.
|
| Cursor on the panel.
|
The list includes.
Molecule Attributes and its components, Atom, bond and residue attributes.
|
| Cursor on the dialog box.
Click on Molecule Attributes. |
The available attributes are listed on the window. |
| click on aromatic display button.
|
For example -
To change the display of aromatic rings, click on the button next to aromatic display.
|
| Click on Disk in the Aromatic ring style option.
|
Select Aromatic ring style as disk.
Click on the color well next to aromatic color. Select color from the color editor. Close the dialog box. |
| Zoom the structure.
Cursor on Aromatic rings. |
Observe the panel.
All the aromatic rings are shown with disks in the center. |
| Type,
rep bs Press enter. |
Change the display of the structure to ball and stick.
rep bs |
| Change the ball scale value to 0.5.
|
On the attributes dialog box, change the Van der Walls radii of the atoms.
Change the value of ball scale to 0.5. Press Enter. |
| Cursor on the panel. | Observe the panel. The atoms are shown with larger atomic radii. |
| Click on Atom Attributes. | Again click on Molecular Attributes check box.
From the list, click on Component Atom Attributes. |
| Select sphere. | In the corresponding window, click on atom style button .
The drop-down menu has many options. Click on sphere to change the display to cpk. Observe the panel. Select dot to bring back the sticks display. |
| Click on Component Bond Attributes. | Now click on Component Bond Attributes.
Here, there are options to change bond style to stick or wire. |
| Click on Component Residue Attributes. | Click on Component Residue Attributes.
Here we have options to change the attributes of the ribbon. |
| Click on Presets menu, change the display to ribbons. | Using presets menu, change the display of the structure on the panel to ribbons. |
| Click on the color well.
Choose a color from the color editor dialog box. Close the color editor dialog box. |
Now, click in the Attribute dialog box,
Now,in the Attribute dialog-box, click on the color well next to ribbon color. Select a ribbon color. And click on close option to close the color editor. |
| Click on ribbon cross-section select edged from the options.
|
There are options to change the cross-section of the ribbon and scaling.
|
| Click on Presets menu, select Interactive 2 option. | Again, change the display to atoms using Presets menu. |
| Cursor on Tools menu. | Attributes can also be changed using Tools menu. |
| Click on Tools menu, scroll down to Structure Analysis .
From the sub-menu select Render by Attribute. |
Click on Tools menu, scroll down to Structure Analysis.
And select Render by Attribute option from the sub-menu. |
| Cursor on the dialog box. | Render by attribute dialog box opens. |
| Cursor on Render by attribute dialog box.
|
Here we have options to change the attributes of atoms, residues, molecules, segmentation regions etc.
Select atoms.
|
| Click on the the Attribute list. | Click on Attribute list to check for available options.
|
| Select bfactor.
|
Choose bfactor.
|
| Slide Number 6
B-factor |
|
| Slide Number 7
B-factor |
PDB file for a protein structure contains B-factor information.
|
| Drag the vertical bars on histogram using mouse.
Fix the white bar at value 50. |
Back to the panel.
The value of B-factor is displayed in the Value text box.
Then fix the white bar at value 50. |
| Cursor on the panel.
Click on color atoms, keep opaque and color surfaces. |
Click on Colors button.
Check options for color atoms, keep opaque and color surfaces. The default color palette is blue and red. You can change the color palette, using drop-down menu. |
| Click Apply. | Click on Apply button. |
| Cursor on the panel. | Observe the panel.
Atoms with high B-factor values are shown in red and least in blue. |
| Cursor on the panel. | As expected, atoms with high B-factors are on the outside of the structure. |
| Cursor on the panel. | Now let us change the attributes of Residues. |
| Select residues in the attributes drop-down in the Render dialog box. | In the Select by Attribute dialog box, click on Attributes button.
From the drop-down, select residues. |
| Cursor on the panel. | Click on Render.
The attributes for residues include kdHydrophobicity scale. |
| Click on kdHydrophobicity from the drop-down menu. | Click on kdHydrophobicity from the drop-down menu.
The values are displayed in the histogram. |
| Slide Number 8
kdHydrophobicity |
|
| Cursor on the panel. | Hydrophobicity of the residues can be shown with colors or worms.
|
| Click on Worms button.
|
Click on Worms button. Click on Apply.
Observe the panel. Worms are modified ribbons that vary in radius. |
| Cursor on the panel. | Most hydrophobic residues face the interior of the structure. |
| Cursor on the panel. | By default, the more hydrophobic residues will be shown with larger radius. |
| Click on worm style to non-worm. Click on OK. | To return the structure to normal ribbon:
|
| Click on File menu, scroll down and click on Close Session option. | Close the Chimera session using File menu. |
| Slide Number 9
Summary |
Let's summarize,
In this tutorial we have learnt to,
|
| Slide Number 10
Assignment |
As an Assignment,
|
| Slide Number 11
Acknowledgement |
* This video summarizes the Spoken Tutorial project
|
| Slide Number 12 |
|
| Slide number 13 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| This is Snehalatha from IIT Bombay signing off.
Thank you for joining. |
