[phenixbb] Ligandfit - problem with ligand_start

Danilo Belviso danilo.belviso at ic.cnr.it
Mon Nov 25 04:25:47 PST 2013

 Dear all,

 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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