[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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