[phenixbb] elbow

Nathaniel Echols nechols at lbl.gov
Thu Jun 13 12:20:47 PDT 2013

On Thu, Jun 13, 2013 at 11:53 AM, Mengbin Chen <mengbinc at 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.

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