[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

-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
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