You can open a terminal window and run elbow as a command line.

phenix.elbow --final_geometry input_file.pdb

Do not forget to initialize the phenix environment, depending on your terminal shell, one example is:

source /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh

Dr Joao Dias

Principal Scientist

Heptares Therapeutics Ltd

BioPark, Broadwater Road,

Welwyn Garden City,

Herts, AL7 3AX

From: Mengbin Chen <[email protected]>
Reply-To: PHENIX user mailing list <[email protected]>
Date: Thursday, 13 June 2013 19:32
To: PHENIX user mailing list <[email protected]>
Subject: [phenixbb] elbow

Dear PHENIX Users,

I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package, but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated!

Thank you in advance,

Mengbin

--
Mengbin Chen

Department of Chemistry

University of Pennsylvania