[phenixbb] elbow

Mengbin Chen mengbinc at sas.upenn.edu
Thu Jun 13 11:32:28 PDT 2013

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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