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
Dear Mengbin,
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
All the best,
Joao
Dr Joao Dias
Principal Scientist
Heptares Therapeutics Ltd
BioPark, Broadwater Road,
Welwyn Garden City,
Herts, AL7 3AX
UK
From: Mengbin Chen
participants (2)
-
Joao Dias -
Mengbin Chen