Dear Dr. Dias, I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation. Thank you, Mengbin On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen wrote:

Dear Dr. Dias,

I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation.

Thank you, Mengbin

On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias wrote:

...

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 Reply-To: PHENIX user mailing list Date: Thursday, 13 June 2013 19:32 To: PHENIX user mailing list 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

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-- Mengbin Chen Department of Chemistry University of Pennsylvania

-- Mengbin Chen Department of Chemistry University of Pennsylvania