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 mailto:[email protected]>
Reply-To: PHENIX user mailing list mailto:[email protected]>
Date: Thursday, 13 June 2013 19:32
To: PHENIX user mailing list mailto:[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
[www.heptares.com]http://www.heptares.com
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please make no use of its contents and contact the sender. Contact and registered office address: Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX. Company No: 06267989
