[phenixbb] find_all_ligands vs. ligand_identification

Nathaniel Echols nechols at lbl.gov
Mon Jun 21 10:16:15 PDT 2010

On Mon, Jun 21, 2010 at 8:13 AM, Mark A Saper <saper at umich.edu> wrote:

> Could someone explain the difference between the GUI
> "ligand_identification" routine and the documented command line
> "find_all_ligands".  The latter appears to have more flexible input
> parameters.

I believe find_all_ligands is just a frontend to LigandFit for searching for
multiple different ligands, which you still need to specify.  The ligand
identification program runs "blind", i.e. it tries all of the most common
ligands in the PDB, or all found in ATP-binding proteins, or everything in a
directory you supply, etc., and would normally be used to fill mystery blobs
in the maps.

> I'm not sure the GUI for ligand_identification is working correctly.

sigh. . .

Yes, someone deleted a couple of essential lines of my code, so it runs in
the wrong directory (and it does still run correctly, but you won't see the
results in the GUI).  I'll send you the patch.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100621/effb406a/attachment-0003.htm>

More information about the phenixbb mailing list