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

Nigel W. Moriarty nwmoriarty at lbl.gov
Wed Aug 20 12:18:52 PDT 2008


What version of PHENIX do you have?

I would recommend using a SMILES string as input to eLBOW if possible.  
In the latest version you can use

phenix.elbow --chemical-components FMN

to run the SMILES string for FMN from the PDB Chemical Components 
database.  It even uses the correct atom names.

In older versions you can get SMILES string from the MSDChem website.  
For FMN its




On 8/20/2008 11:54 AM, Feldman III, George Franklin wrote:
> 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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> phenixbb at phenix-online.org
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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