Autobuild with ligand in place?
Hallo! Sorry for the probably easy question. 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? Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Via Ferrata, 1 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969
On Thu, Apr 15, 2010 at 5:46 AM, Claudia Scotti
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
participants (2)
-
Claudia Scotti -
Nathaniel Echols