On Thu, Jun 13, 2013 at 11:53 AM, Mengbin Chen <mengbinc@sas.upenn.edu> wrote:

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.

This has nothing to do with use of the GUI versus command line - the problem is that using a PDB file as the only source of chemical information is unlikely to work, especially if no hydrogens are present. �At the very least you need explicit hydrogens, and ideally you need an input file that actually defines the topology, like SMILES or MOL2 or CIF. �If it's a ligand that is already in the PDB you can just give it the three-letter code and it will extract this information automatically from the database included with Phenix.

I guess I need to add a warning to the GUI if users try to use a PDB file alone, because this problem comes up again and again.

-Nat

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