Hi, I am trying to open the same pdb file twice and apply mm command on the chains. The following script loops through the files in the folder so i open the same pdb twice: #!/bin/bash for file in `ls tmp_d2` do chimera --nogui --silent tmp_d2/$file tmp_d2/$file tmp_d2/$file tmp_d2/$file chim.cmd > test_A.pdb mv test_A.pdb temper/$file echo "$file" done File "chim.cmd" has the following: mm #0:.A:.B #1:.B:.A pair ss measure rotation #0 #1 I get the following error: 1c9o_1.pdb Error while sourcing chim.cmd, line 1: "measure rotation #0 #1" Rotation angle is near zero (0 degrees) I should be getting an angle of 180 degrees because they are all dimers. I have two versions of chimera on my system 1.7 and 1.11.2, does that make a difference? Thank you. Regards, Kavya Shankar