reinitialize
fetch 4v50
#open bS21 pdb file using file bar

#AU=bS21 in E coli ribosome
hide all
show cartoon, chain AU
color red, chain AU

align 4v50 & chain AU, bS21_2_alphafold & chain A

set_view (\
    -0.244961798,   -0.963306785,   -0.109717429,\
    -0.320884526,    0.187341690,   -0.928406119,\
     0.914892435,   -0.192216620,   -0.354998559,\
    -0.000000000,    0.000000000, -153.778854370,\
    -3.215358734,    2.434379578,   -1.995119095,\
   121.240417480,  186.317291260,  -20.000000000 )

align bS21_1_alphafold & chain A, bS21_2_alphafold & chain A
align bS21_2_alphafold & chain A, bS21_3_alphafold & chain A

#compare b subtilis ribosome to e coli ribosome
reinitialize
fetch 4v50
fetch 7QV3

hide all
show cartoon, 4v50 & chain AU
color red, 4v50 & chain AU
show cartoon, 7QV3 & chain b
color blue, 7QV3 & chain b

align 4v50 & chain AU, 7QV3 & chain b

#align by 16S instead of by bS21
reinitialize
fetch 4v50
fetch 7QV3

color salmon, 4v50
show cartoon, 4v50 & chain AU
color red, 4v50 & chain AU
color lightblue, 7QV3
show cartoon, 7QV3 & chain b
color blue, 7QV3 & chain b

align 4v50 & chain AU, 7QV3 & chain b
