#this script defines basic elements from ILE-tRNA and generates image of #ILE-tRNA with colored helices, non-Watson-Crick hydrogen bonds and anticodon. #Color of helices is corresponding with their color in text of credit work. #To see a nice picture first open file 1ffy.pdb! #defining and echoing part: define helix1 1-7T or 66-72T define helix2 10-13T or 22-25T define helix3 26-32T or 38-44T define helix4 49-53T or 61-65T #this script cannot define as "helices" all of them, because this name was #already given by RasMol to another multitude. That's why it will be define #as "helixes". define helixes (helix1 or helix2 or helix3 or helix4) echo New names for spiral parts of tRNA were given: echo helix 1 - for acceptor stem; echo helix 2 - for D-stem; echo helix 3 - for anticodon stem; echo helix 4 - for T-stem; echo helixes - for their combine! echo OI-WAY! define loop1 14-21T define loop2 33-37T define loop3 45-48T define loop4 54-60T define loops (loop1 or loop2 or loop3 or loop4) echo For loops were just given the following names: echo loop1 - for D-loop; echo loop2 - for anticodon loop; echo loop3 - for variable loop; echo loop4 - for T-loop; echo loops - for all of them! echo OI-WAY!! echo define knot1 8T or 14T define knot2 15T or 48T define knot3 50T or 64T define knot4 54T or 58T define knots (knot1,knot2,knot3,knot4) echo Not canon, but base-pairs are now defined as knots! echo Information about them I have taken from PDB-file, REMARK 103... echo define lends 73-74T echo Unpaired 3'-ending of tRNA is define as lends! define anticodon 34-36T echo 3 nucleotides of anticodon loop are now define as anticodon! echo OI-WAY!!! echo #show-part lays below... center 23T zoom 1400 rotate x 60 rotate y -70 restrict rna color white backbone 50 echo To have a colored show, press ENTER and go on pressing! echo pause select helix1 color yellow echo Now the acceptor stem appear! pause select helix2 color cyan echo D-stem were colored cyan! pause select helix3 color green echo The anticodon stem is green! pause select helix4 color pink echo The last T-stem appear pinky! pause select knots and not phosphorus color blue echo Not canon base-pairs were colored blue. pause select anticodon color red echo Anticodon is in red now! echo OI-WAY!!!!