User:Shai Biran/Practice Proteopedia tutorial shai6
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| - | Now we want to select the segment of the protein that runs through the barrel and color it green. | ||
| - | To make a selection, click on the “selections” tab. | ||
| - | We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment. | ||
| - | Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in. | ||
| - | [[Image:Hover_over_atom.png]] | ||
| - | + | [[Image:Limit_to_residue_number.png]] | |
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| + | With the chain segment selected, it’s time to change its color to match the image in the Molecule of the Month. | ||
| + | Click on the “colors” tab of the Scene Authoring Tools. Click on a lime color in the color palette to change the color of the selected chain segment. Turn off selection halos to better view the change in color. | ||
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| + | [[Image:Colors.png]] | ||
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| + | Now let’s make the background black. | ||
| + | In the section titled “color”, mark the button next to “background”. Now any color you select from the color palette will affect the background instead of the selection. | ||
| + | Click on the color black in the color palette. | ||
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| + | [[Image:Black_Bckgrnd.png]] | ||
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| + | All that’s left is to show the chromophore and color it in the CPK scheme. | ||
| + | Click on the “selections” tab. In the input box under “limit to residue types:” type “CRO”. (In the PDB file, the chromophore is listed as a residue with type “CRO”) | ||
| + | Click on the “replace selection” button. Turn on selection halos. | ||
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| + | [[Image:Selecting_CRO.png]] | ||
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| + | Click on the “representations” tab. | ||
| + | In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button. | ||
| + | Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”. | ||
| + | Turn off selection halos to better view the new color. | ||
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| + | [[Image:CRO_in_CPK.png]] | ||
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| + | Notice that connection between the chromophore & the chain is missing, but is seen in the original picture: [[User:Shai Biran/GFP test page]]. Let’s '''visualize''' those missing bonds in the chain. | ||
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| + | Click on the “selections” tab; in the ‘build your selection’ box, under ‘groups’ select ‘backbone/mainchain’; In the input box under “limit to residue numbers:” type “64,68”. (These are the numbers of the residues directly preceding and following the chromophore.) Click on the “add to selection” button. Click on the “representations” tab. In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button. Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”. | ||
| + | Turn off selection halos to better view the new color. | ||
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== Next == | == Next == | ||
| + | |||
| + | [[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]] | ||
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| + | [[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]] | ||
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| + | == References == | ||
| + | <references/> | ||
Current revision
Adding a GREEN SCENE LINK
With the chain segment selected, it’s time to change its color to match the image in the Molecule of the Month.
Click on the “colors” tab of the Scene Authoring Tools. Click on a lime color in the color palette to change the color of the selected chain segment. Turn off selection halos to better view the change in color.
Now let’s make the background black.
In the section titled “color”, mark the button next to “background”. Now any color you select from the color palette will affect the background instead of the selection.
Click on the color black in the color palette.
All that’s left is to show the chromophore and color it in the CPK scheme. Click on the “selections” tab. In the input box under “limit to residue types:” type “CRO”. (In the PDB file, the chromophore is listed as a residue with type “CRO”) Click on the “replace selection” button. Turn on selection halos.
Click on the “representations” tab. In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button. Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”. Turn off selection halos to better view the new color.
Notice that connection between the chromophore & the chain is missing, but is seen in the original picture: User:Shai Biran/GFP test page. Let’s visualize those missing bonds in the chain.
Click on the “selections” tab; in the ‘build your selection’ box, under ‘groups’ select ‘backbone/mainchain’; In the input box under “limit to residue numbers:” type “64,68”. (These are the numbers of the residues directly preceding and following the chromophore.) Click on the “add to selection” button. Click on the “representations” tab. In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button. Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”. Turn off selection halos to better view the new color.
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