# Open bound and unbound conformations, before transfer. 11 & 00 means with leu addded to avoid Ade87 rotation open lams_finalABstate11.pdb open p21a_withlamsstate00.pdb # Show ribbons and ligand. preset apply int 1 # Create morph #1 -> #0 as #2. morph start #1 frames 45 morph interpolate #0 frames 45 morph movie nogui true # Hide unbound model, bound state ribbon, and show just ligand atoms. ~modeldisplay #1 ~ribbon #0 show ligand # Show morph in bound state, last frame. coordset #2 -1 # Show residues of morph near ligand, hide leucine atoms and ribbon show #2 & ligand zr<3; ~ ribbon #2:88.b; ~ show #2:88@c,n,o,ca,cb,cg,cd1,cd2; # Show last base of RNA, #show #2:87.b; repr bs #2:87.b; color byelement #2:87.b; color grey #2:88.B; # Return morph to unbound state, first frame. coordset #2 1 # Color background, morph ribbon, and ligand. set bg_color white color yellow,r #2:1-860.a color purple,r #2:149-194.a color aquamarine,r #2:225-419.a color plum,r #2:569-628.a color firebrick,r #2:629-794.a color orange,r #2:795-860.a color blue,r #2:1-87.b modelcolor white ligand # Ligand in ball and stick style. repr bs ligand # Turn on silhouette edges. set silhouette set silhouette_width 1.5 # Increase subdivision quality to 5 for smoother ribbon, atoms, bonds. set subdivision 5 # Name full view position savepos closeview # Zoom out, move molecule to corner, name position. scale 0.7 move x -20 move y -10 savepos wideview # Move ligand away and rotate it some, name position. ~select 2 move x 60 move y 40 turn z 90 turn x 90 select 2 savepos farligand # Add caption. 2dlabel create title text "Aminoacylation functional cycle" size 38 style bold xpos 0.3 ypos 0.98 color forest green 2dlab create enzyme text "E. coli LeuRS" size 24 style bold xpos .12 ypos .59 color black 2dlab create trna text "tRNA" size 24 style bold xpos .12 ypos .54 color blue # Start recording ADD SUPERSAMPLE FOR QUALITY movie record directory /midterm/palencia/tmp/ supersample 3 # Play movie sequence reset wideview 50 wait 50 reset closeview 50 wait 50 2dlabel change title visibility hide frames 25 2dlabel change enzyme visibility hide frames 25 2dlabel change trna visibility hide frames 25 wait 25 # Add labels and Play morph 2dlab create morphlab text "conformational changes..." size 24 style bold color forest green xpos .1 ypos .75 visibility hide 2dlab change morphlab visibility show frames 25 wait 25 2dlab change morphlab visibility hide frames 25 wait 25 coordset #2 1,46,1; wait 46 2dlab change morphlab visibility show frames 25 wait 25 2dlab change morphlab visibility hide frames 25 wait 25 ~disp ligand; wait coordset #2 45,1,-1; wait 45 wait 25 disp ligand; wait coordset #2 1,46,1; wait 46 wait 25 # Show hydrogen bonds/ hide hbonds, roll and stop movie scale 1.03 25 wait 50 hbond intermodel true intramodel false color green linewidth 5; wait wait 50 roll y 1 78; wait wait 25 roll y -1 85; wait wait 25 ~hbond intermodel true intramodel false color green linewidth 5; wait wait 25 movie stop #load states for making transfer (#3 and #4) open lams_finalABstate2.pdb open p21a_withleutRNAstate3.pdb # Show ribbons and ligand. preset apply int 1; wait # Create morph #3 -> #4 as #5. morph start #3 name 2ndmorph frames 45; wait morph interpolate #4 name 2ndmorph frames 45; wait morph movie nogui true name 2ndmorph; wait # Add caption for transfer. 2dlab create transfer text "transfer of leucine to tRNA..." size 24 style bold color forest green xpos .1 ypos .75 visibility hide 2dlab change transfer visibility show frames 25; wait 2dlab create releaseamp text "AMP release..." size 24 style bold color forest green xpos .1 ypos .7 visibility hide 2dlab change releaseamp visibility show frames 25; wait wait 25 # Hide unbound model, bound state ribbon, and show just ligand atoms(Ade87 & leu). ~modeldisplay #0-4; wait show #5:87-88.b # load AMP to see releaseAMP as #7, represent color, save position open 7 lams_finalABAMPout.pdb repr bs #7; color white #7; color byelement #7; wait wait 25 savepos ampout # show morph in bound state or last frame 1st morph, and Show residues near ligand(same as before). coordset #5 -1; show #2 & ligand zr<3; wait # Show/return morph#5 in catalytic site, 1st frame. coordset #5 1 # Show last base of RNA + leu (ball & stick) repr bs #5:87-88.b; color byelement #5:87.b; color white #5:88.b # Color background, morph ribbon, and ligand. set bg_color white; wait color yellow,r #5:1-860.a; wait color purple,r #5:149-194.a; wait color aquamarine,r #5:225-419.a; wait color plum,r #5:569-628.a; wait color firebrick,r #5:629-794.a; wait color orange,r #5:795-860.a; wait color blue,r #5:1-87.b; wait # Turn on silhouette edges. set silhouette set silhouette_width 1.5 wait 20 # Name full view position savepos closetransfer # Start recording, show amp out ADD SUPERSAMPLE FOR QUALITY movie record directory /midterm/palencia/tmp/ supersample 3 wait 50 reset ampout 75 wait 75 # Play morph coordset #5 1,46,1; scale 0.99 80; wait 46 ~disp ligand; wait coordset #5 45,1,-1; wait 45 wait 25 disp ligand; wait coordset #5 1,46,1; wait 46 wait 25 # hide label of transfer 2dlab change transfer visibility hide frames 25 2dlab change releaseamp visibility hide frames 25 wait 25 # roll a bit and stop movie ###scale 1.03 25 ###wait 50 ###hbond intermodel true intramodel false color green linewidth 5; wait roll y 1 75; wait wait 25 roll y -1 75; wait wait 25 movie stop # load #6, same with tRNA far open p21a_withleutRNAout.pdb # Show ribbons and ligand. ~select 7 preset apply int 1 # repr last base rna + leu show #6:87-88.b repr bs #6:87-88.b; color byelement #6:87.b; color white #6:88.b # Color background, morph ribbon, and ligand. set bg_color white; wait color yellow,r #6:1-860.a; wait color purple,r #6:149-194.a; wait color aquamarine,r #6:225-419.a; wait color plum,r #6:569-628.a; wait color firebrick,r #6:629-794.a; wait color orange,r #6:795-860.a; wait color blue,r #6:1-87.b; wait # Turn on silhouette edges. set silhouette set silhouette_width 1.5 wait 20 # name position, fartrnaleu ~modeldisplay #5; wait repr bs #7; color white #7; color byelement #7; wait 2dlab create releasetrna text "release of Leu-tRNA ..." size 24 style bold color forest green xpos .1 ypos .74 savepos fartrnaleu wait 20 movie record directory /midterm/palencia/tmp/ supersample 3 wait 25 # moving trnaleu away reset fartrnaleu 100 2dlab change releasetrna visibility hide frames 25; 2dlab change releaseamp visibility hide frames 25 2dlab change title visibility show frames 25 wait 50 # Extra stationary frames at end avoid compression artifacts on last frame. wait 20 # Stop recording and encode movie. CHANGE BITRATE FOR QUALITY movie stop movie encode mformat avi qscale 1 output ~/Desktop/amino_final.avi