Protein Structure - Revision history

Carol: /* Structure comparisons */

2025-10-07T08:33:35Z

Structure comparisons

← Older revision		Revision as of 10:33, 7 October 2025
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	'''Question 6.''' Can you explain what is the main difference of the crystal structures, the predicted structure and the modelled structure with SWISS-MODEL? Which one do you think would be more reliable?		'''Question 6.''' Can you explain what is the main difference of the crystal structures, the predicted structure and the modelled structure with SWISS-MODEL? Which one do you think would be more reliable? Here you are encouraged to use a chatbot to ask for hints, like chatGPT, but you will have to justify your selection.

Carol: /* Visualization & PyMOL */

2025-10-07T08:13:06Z

Visualization & PyMOL

← Older revision		Revision as of 10:13, 7 October 2025
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	In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''br.''.		In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''br.''.

	'''Hint:''' ~~We will use~~ select ZZ,''br''.(XX ''around'' 6) if we ~~want to~~ select all residues in a distance of 6Å to XX, and name this new objext ZZ		'''Hint:''' ''select'' ZZ, ''br''.(XX ''around'' 6) With this command we can select all residues in a distance of 6Å to XX, and name this new objext ZZ


	'''Question 4.''' Now colour the epitope in red and provide a screenshot. How many residues can you count that are in close contact with the IgE antibody?		'''Question 4.''' Now colour the epitope in red and provide a screenshot. How many residues can you count that are in close contact with the IgE antibody?


	== Structure comparisons ==		== Structure comparisons ==

Carol at 08:11, 7 October 2025

2025-10-07T08:11:52Z

← Older revision		Revision as of 10:11, 7 October 2025
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	⇒ Now we want to colour which specific residues of the allergen are in close contact with the antibody (exactly at a distance of 4Å). We will call this object the “epitope”. To define the distance, we can use the command ''around''.		⇒ Now we want to colour which specific residues of the allergen are in close contact with the antibody (exactly at a distance of 4Å). We will call this object the “epitope”. To define the distance, we can use the command ''around''.

	In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''~~byres~~''.		In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''br.''.

	'''Hint:''' We will use ''~~byres~~''.(XX ''around'' 6) if we want to select all residues in a distance of 6Å to XX		'''Hint:''' We will use select ZZ,''br''.(XX ''around'' 6) if we want to select all residues in a distance of 6Å to XX, and name this new objext ZZ

Carol at 08:09, 7 October 2025

2025-10-07T08:09:05Z

← Older revision		Revision as of 10:09, 7 October 2025
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	⇒ Colour the different chains of the antibody (IgE) in yellow and blue and the allergen (Hev b 8) in green.		⇒ Colour the different chains of the antibody (IgE) in yellow and blue and the allergen (Hev b 8) in green.


			'''Hint: To colour chain A, you can do it on the command line by the command color -> color red, chain A.'''


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	'''Question 4.''' Now colour the epitope in red and provide a screenshot. How many residues can you count that are in close contact with the IgE antibody?		'''Question 4.''' Now colour the epitope in red and provide a screenshot. How many residues can you count that are in close contact with the IgE antibody?


	== Structure comparisons ==		== Structure comparisons ==
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	To align the two chains, we can use the command ''align''. The align command requires two elements to align.		To align the two chains, we can use the command ''align''. The align command requires two elements to align separated by comma.

Carol: /* Visualization & PyMOL */

2025-10-07T08:01:17Z

Visualization & PyMOL

← Older revision		Revision as of 10:01, 7 October 2025
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	[[Image:PyMOL_panels.png\|thumb\|center\|border\|400px\|'''Figure 3.''' The PyMOL Panels.]]		[[Image:PyMOL_panels.png\|thumb\|center\|border\|400px\|'''Figure 3.''' The PyMOL Panels.]]


			'''Important Note: In this exercise, you will do some command line coding and get some outputs on the PyMOL. Please remember to add your code into the answer along with the screenshot.'''

	⇒ Now select the best complex and load it into PyMOL using the ''fetch'' command.		⇒ Now select the best complex and load it into PyMOL using the ''fetch'' command.

Carol at 20:35, 6 October 2025

2025-10-06T20:35:34Z

← Older revision		Revision as of 22:35, 6 October 2025
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	Under the "objects panel on the right you will see some quick buttons including "3-button Viewing, and magic wand, SEQ, and a camera to record videos. Make sure you have the SEQ button activated to show your sequence.		Under the "objects panel on the right you will see some quick buttons including "3-button Viewing, and magic wand, SEQ, and a camera to record videos. Make sure you have the SEQ button activated to show your sequence.

			[[Image:PyMOL_show_SEQ.png\|thumb\|center\|border\|400px\|'''Figure 4.''' The PyMOL Structure of 9NUE. A subsection of Chain A is displayed in grey.]]


	⇒ Scroll where you can see the sequence name, which name has the new profilin in PyMOL?		⇒ Scroll where you can see the sequence name, which name has the new profilin in PyMOL?

Carol: /* Visualization & PyMOL */

2025-10-06T20:12:22Z

Visualization & PyMOL

← Older revision		Revision as of 22:12, 6 October 2025
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	* The "objects panel" on the right, with a list of all your objects and with the pull-down menus to show (S) or hide (H) elements		* The "objects panel" on the right, with a list of all your objects and with the pull-down menus to show (S) or hide (H) elements
	* The "command-line panel" in the bottom, where you can type commands		* The "command-line panel" in the bottom, where you can type commands

			[[Image:PyMOL_panels.png\|thumb\|center\|border\|400px\|'''Figure 3.''' The PyMOL Panels.]]


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	'''Question 2.''' Provide a screenshot of the complex.		'''Question 2.''' Provide a screenshot of the complex.


	~~[[Image:RGAE_active_site.png\|thumb\|center\|border\|400px\|'''Figure 3.''' The active site in RGAE.]]~~

Carol: /* Visualization & PyMOL */

2025-10-06T20:07:05Z

Visualization & PyMOL

← Older revision		Revision as of 22:07, 6 October 2025
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	* The "viewer panel" where the molecule will be displayed		* The "viewer panel" where the molecule will be displayed
	* The "objects panel" on the right, with a list of all your objects and with the pull-down menus to show (S) or hide (H) elements		* The "objects panel" on the right, with a list of all your objects and with the pull-down menus to show (S) or hide (H) elements
	* The ~~'''~~command-line panel~~'''~~ in the bottom, where you can type commands		* The "command-line panel" in the bottom, where you can type commands

Carol: /* Overview */

2025-10-06T19:59:04Z

Overview

← Older revision		Revision as of 21:59, 6 October 2025
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	Therefore today we are going to start with a biological question we want to answer:		Therefore today we are going to start with a biological question we want to answer:

	'''Why only plant profilins are giving an allergic response despite their high conservation across species?		'''Why only plant profilins are giving an allergic response despite their high conservation across species? Why are we not allergic to mammal profilins, for example?'''
	Why are we not allergic to mammal profilins, for example?'''

	== A bit of background ==		== A bit of background ==

Carol: /* Overview */

2025-10-06T19:58:45Z

Overview

← Older revision		Revision as of 21:58, 6 October 2025
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	Therefore today we are going to start with a biological question we want to answer:		Therefore today we are going to start with a biological question we want to answer:

	Why only plant profilins are giving an allergic response despite their high conservation across species?		'''Why only plant profilins are giving an allergic response despite their high conservation across species?
	Why are we not allergic to mammal profilins, for example?		Why are we not allergic to mammal profilins, for example?'''

	== A bit of background ==		== A bit of background ==