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Biochemistry student intro
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== Start your PyMOL == Start your shortcut to PyMOL "C:\Python27\PyMOL\PyMOL.exe"<br> Now click and do the following: # Write in command line: '''fetch 1lev''' # Right Menu: -> 1lev -> "A" -> preset -> Publication # Top Menu: Display -> Sequence # Top Menu: Display -> Sequence Mode -> Chains # In Sequence, select so all "F" is marked. # Right Menu: -> (sele) -> "A" -> remove atoms. (1LEV is crystallized in dimer formation. So we only need to view 1 chain) # Top Menu: Display -> Sequence Mode -> Residue Codes # In Sequence, select so only substrate (F6P) is marked (A/338) # Right Menu: -> (sele) -> "A" -> zoom # Right Menu: -> (sele) -> "A" -> rename selection -> f6p # Right Menu: -> (f6p) -> "C" -> by element -> Select to Carbon is not green # Right Menu: -> (f6p) -> "A" -> find polar contacts -> to others excluding solvent # In Sequence, select so only MN is marked (A/340) # Right Menu: -> (sele) -> "A" -> rename selection -> mn # Right Menu: -> (mn) -> "S" -> spheres # Write in console: '''select act_site, byres f6p around 3.5''' # Right Menu: -> (act_site) -> "S" -> sticks # Right Menu: -> (act_site) -> "L" -> residues # Top Menu: Display -> Background -> White # Find a good view, and push "Ray" in the top right of the grey command console. # Top Menu: File -> Save Image As -> PNG # Put it into your student article
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