PyMOL Quickie Extending Secondary Structure

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Extending a beta sheet of a protein • 00:01:03 Generating and linking secondary struture • 00:11:47 Extending secondary structure • WARNING, PyMOL is not the correct piece of software to generate structures de novo, this should only be used for exploring ideas and making images. • ################################### • first . . . making a beta sheet # • ################################### • fab (https://pymolwiki.org/index.php/Fab) • fab PEPTIDE, new-obj1, ss=1 # helix • fab PEPTIDE, new-obj2, ss=2 # antiparallel • fab PEPTIDE, new-obj3, ss=3 # parallel • align new-obj2, new-obj3 • ########################### • switch to editing mode # • translate and rotate • hold [shift] and left-click-drag to rotate • hold [shift] and middle-click-drag to translate • add liking residues • hold [alt] and type amino-acid single letters • move chain • Build : Sculpting : Auto-Sculpting • hold [ctl] and left-click-drag to move chain • ########################### • switch to viewing mode # • select terminal hydrogen • remove sele • check length of chain, add to residue number of chain 2 • alter sele, resi=str(int(resi)+11) • extract to single object • select all • (sele) : [A] : extract object • ########################### • switch to editing mode # • pick C and N of respective chains • bond • • • ########################## • Extending a beta sheet # • ########################## • rein • fetch 5w3x_B • remove ! polymer • make a selection • copy to new object • re-color • ########################### • switch to editing mode # • translate and rotate • hold [shift] and left-click-drag to rotate • hold [shift] and middle-click-drag to translate • ########################### • switch to viewing mode # • select old loop • remove sele • check chain numbering and adjust, add to residue number of chain 1 and 2 • alter sele, resi=str(int(resi)+2) • alter sele, resi=str(int(resi)+4) • extract to single object • select all • (sele) : [A] : extract object • ########################### • switch to editing mode # • pick C and N of respective chains • bond

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