[phenixbb] Ligandfit - problem with ligand_start
danilo.belviso at ic.cnr.it
Mon Nov 25 04:25:47 PST 2013
I am working on a membrane protein bound to a antenna molecule: I know
that the molecule binds to lysine residue but I do not know how many and
which lysine residues it binds. 20 diffraction datasets of
protein-ligand complex have been obtained and now, I would quickly
localize the ligand using the Fo-Fc map of each data set and using the
information on the covalent bound protein-ligand.
Ligandfit tool (PHENIX) seems to be indicated to do this; to use the
information on the covalent bound, I have thought to use the
ligand_start keyword with a pdb containing a ghost atom (however present
in ligand model) perfectly superposed to the lysine atom that should
bind the ligand.
The command used is:
phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb
ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \
refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif
- prot.mtz (data)
- prot.pdb (protein without ligand)
- lig.pdb (ligand containing ghost atom)
- lig_start.pdb (ghost atom superpose to NZ of a lysine)
- lig.cif (restrain of lig.pdb)
At the end of the processing, ligand is not found. So, I have tryed
with ligand_cc_min=0.01, but also in this case ligandfit does not give
result. I have thought that no ligand is present. However, to be sure
that all was correct, I have run the same command by using an other
protein where an other ligand has been correctly fitted. Also in this
case, no result has been obtained. Conversely, without the use of
ligand_start, ligandfit properly localizes the ligand.
I'm doing some mistake in the use of ligand_start?
Thanks for your answers.
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