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2_ex
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ex workshop 3
-------------------
EX 6
PyMOL> fetch 2JQY
PyMOL> split_states 2JQY (https://pymolwiki.org/index.php/Split_states (Links to an external site.)Links to an external site.)
You will now see 10 conformers each in a separate object
PyMOL> hide all
PyMOL> show cartoon
The differences are mainly in the loops on the surface of the barrel structure.
2JQY_split_states.png
You may color these differently to see the differences even better.
Click all (layers) to hide them and only show object 2JQY_0001 by clicking on the object name.
PYMOL> fetch 2IWW
PyMOL> hide all
PyMOL> show cartoon, 2IWW + 2JQY_0001
PyMOL> hide cartoon, 2IWW and chain B
PyMOL> align 2IWW and chain A, 2JQY_0001
PyMOL> zoom
2JQY_align.png
Rotate the structures and take a closer look at the flexible loop which can close the channel (barrel structure).
Also nice visualization in surface representation:
PyMOL> show surface
Color each structure differently. Optionally also color the loop to make to difference more clear.
PyMOL> color ..., 2IWW and resi 219-232
File » Save Session As…
PyMOL> delete 2JQY_* (this will remove all conformers and only keep object 2JQY)
-------------------------------------------------------------------------------------------------------------------------------------------------------
PyMOL> fetch 1Q55
PyMOL> hide all
PyMOL> show cartoon
PyMOL> create calcium, 1Q55 and chain A+B and resn CA
PyMOL> show spheres, calcium
PyMOL> color firebrick, 1Q55 and chain A
PyMOL> color skyblue, 1Q55 and chain B
PyMOL> create trparm, 1Q55 and resi 2
PyMOL> show sticks, trparm
PyMOL> set valence, 0
PyMOL> show surface, 1Q55 and chain A
The N-terminal adhesion arm of one chain is inserted into the other chain (termed strand swapping) using the Trp (W2) as anchor residue into a hydrophobic pocket.The surface representation is somehow weird because chain A is "opened" by chain B. This will not be the case if you put the chains in different objects.
PyMOL> create chaina, 1Q55 and chain A
PyMOL> create chainb, 1Q55 and chain B
Click on the object 1Q55 to hide.
PyMOL> set transparency = 0.2
-------------------------------------------------------------
stippellijntjes weg:
setting --> cartoon --> gap cutoff --> 0