open 1quv delete solvent # the following command removes the residues from the main surface and puts # them in a different "surface category" named "loop" surfcat loop :15-41 # then just show the main surface surf ribbon loop color blue,r ~disp # can use "loop" in findclash command, with options to select and color # the clash atoms (red by default), but not to draw lines (make false) findclash loop overlap 0.01 select true color true make false # promote selected atoms to whole residues for display sel up disp sel ~sel preset apply pub 1 col byatom loop