[phenixbb] placing ligands in coot with phenix.elbow output

Feldman III, George Franklin gfeldman at indiana.edu
Wed Aug 20 11:54:39 PDT 2008

Hi all,

I am having difficulties with my ligand. My ligand is an FMN (flavin 
mononucleotide) and its pdb file was originally created using PRODRG. I 
used the DRGFIN.PDB output file to run elbow (phenix.elbow DRGFIN.PDB 
--opt). The output contains hydrogens, which as we all know do not work 
well with coot. So when I try to place my ligand in its correct 
position and save the coordinates in coot, I get an error of duplicated 
atom labels when trying to merge the molecule to the ligand using 
phenix.refine. I tried using the command "phenix.elbow DRGFIN.PDB --opt 
--write-hydrogens=False" but phenix told me that last command doesnt 
exist (although its posted on the web page). Manually changing the atom 
names will affect both the connectivity and the cif file (I think), so 
it is an option I would rather avoid. Is there a way around all of this?

Best Regards,
George (Trey) Feldman

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