Hello Elaine, I have been trying to save a protein-ligand complex in pdb format with the command line,but i haven't successful doing so. I have tried using write, display, select command but nothing worked. Steps that i followed: Open the NoH.pdb file in chimera With command line: cd /home/Desktop/test/Cmd_Tango_Dock/OUT/1abe.pdb/tmpO9IqaJ viewdock rigid_ranked.mol2 "Dock 4, 5 or 6" combine #0,1.1 111_#name.pdb-I used this command to save my result. If you could tell me what mistake I am making in saving the file. Thank You Regards Preet ------------------------------------------------------------------------------------------------------------ [ C-DAC is on Social-Media too. Kindly follow us at: Facebook: https://www.facebook.com/CDACINDIA & Twitter: @cdacindia ] This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------