[phenixbb] elbow

[Joao Dias]

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 <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

--
Mengbin Chen
Department of Chemistry
University of Pennsylvania


[www.heptares.com]<www.heptares.com><http://www.heptares.com>




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