[phenixbb] Autobuild with ligand in place?

Nathaniel Echols nechols at lbl.gov
Thu Apr 15 06:34:52 PDT 2010

On Thu, Apr 15, 2010 at 5:46 AM, Claudia Scotti
<claudiascotti at hotmail.com>wrote:

> I'm trying to rebuild a model with Autobuild. The protein has a ligand,
> whose density is already well defined, thus that the input for the new
> autobuild run includes its coordinates as well.
> When I start the autobuild run, however, I see that the ligand is removed
> before rebuilding, which leads the program to use the ligand density to try
> to rebuild loops, thus introducing errors.
> How can I keep the ligand in place, please? Or is there any alternative
> solutions?

I believe the answer is to move the ligand to a separate PDB file, and add
these parameters:


(Or if you're using the GUI, add the ligand PDB file and change the type to
"Ligands", and uncheck Settings->Input files->Keep pdb atoms.

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