[phenixbb] Autobuild with ligand in place?

[Nathaniel Echols]

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:

input_files.input_lig_file_list=ligand.pdb
input_files.keep_pdb_atoms=False

(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.

-Nat
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100415/120a75f8/attachment-0003.htm>