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PyMOL Quickie - Extending Secondary Structure

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