[phenixbb] elbow

Joao Dias joao.dias at heptares.com
Thu Jun 13 11:42:04 PDT 2013

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,

Dr Joao Dias
Principal Scientist

Heptares Therapeutics Ltd
BioPark, Broadwater Road,
Welwyn Garden City,
Herts, AL7 3AX

From: Mengbin Chen <mengbinc at sas.upenn.edu<mailto:mengbinc at sas.upenn.edu>>
Reply-To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Date: Thursday, 13 June 2013 19:32
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
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 Chen
Department of Chemistry
University of Pennsylvania


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