If a protein was designed as a closed cyclic protein (N-and C-terminus closed after reaction), can PyMOL show this structure? Because in PyMOL, the sequence is always linear, so how the closed cyclic protein looks like in PyMOL?
Not by default, at least not for the cartoon representation. You can trick it to do so by overlaying a model of the original peptide with a cyclic permutation of the peptide: cut-and-paste the coordinates of first half of the peptide to the end of the coordinate block in the pdb file and renumber the residues. Create the image by displaying parts of the two models with a one amino acid overlap at the switchover points - you may have to play around a bit to put the switchover points to positions where they produce no noticeable artefacts.
For a stick representation, you can probably get away with just defining the ring-closure bond using the "bond" command https://pymolwiki.org/index.php/Bond
Annemarie Honegger Thanks so much for the details for the explanations, it really helps me to some extent to draw the closed circular protein. However, the N, C-terminus were split, so the structures in cartoon are not always highly overlopped to the part from cut-and-paste coordinations, although the sticks-shown structures are same.
What is why you have to choose the splice point between the model representations carefully - it is best to put it at the boundary between two secondary structure elements. To demonstrate (copy-paste the commands into the pymol command line:
fetch 1ubq, ubq1
fetch 1ubq, ubq2
util.cbss("ubq1","red","yellow","green",_self=cmd)
util.cbss("ubq2","red","yellow","green",_self=cmd)
This places the splice point within the beta-strand -bad:
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show cartoon, /ubq1///1-6
show cartoon, /ubq2///6-33
This within the coil -bad kink:
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show cartoon, /ubq1///1-19
show cartoon, /ubq2///19-33
this within the helix -bad:
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show cartoon, /ubq1///1-27
show cartoon, /ubq2///27-33
putting it at the boundary between sheet and coil:
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show cartoon, /ubq1///1-17
show cartoon, /ubq2///17-33
or between coil and helix:
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show cartoon, /ubq1///1-23
show cartoon, /ubq2///23-33
the break point is much less noticeable.
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