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.

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first . . . making a beta sheet #
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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

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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 #
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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