Hi Jack, Sorry it may be a little bit confusing.  To use LigandFit parameters in ligand_identification,the parameter group (bold text in documentation) should be added to the keywords. In your case, you'd use: search_target.search_center="-12.59711.99021.741" search_parameters.number_of_ligands=6 The rest will remain the same. I'll update the documentation to make it clearer.  Feel free to email me with any questions. Best, Li-Wei On 3/31/2021 1:25 PM, Tanner, John J. wrote:

Phenix BB:

I would like to use phenix.ligand_identification to analyze an electron density feature in the active site of an enzyme; however, I do not see how to specify search_center in the gui. Thus, the program places the ligands into a strong density feature on the surface of the protein. When I run it from the command line with search_center specified, it seems to ignore the search center coordinates and again places the ligands into the density feature on the surface. My command script:

[tannerjj@europa ligandID]$ cat ligandID.com

phenix.ligand_identification \

mtz_in = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.mtz" \

mtz_type = diffmap \

input_labels = "FOFCWT PHFOFCWT" \

ligand_list = "DPR PRO HYP HZP UYA UY7" \

model = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.pdb" \

ncpu = 4 \

output_dir = "/titan/tanner/MmP5CDH/THLP/ligandID/temp" \

number_of_ligands = 6 \

job_title = "THLP8-1_003 D,L-Pro and 4 OH-Pro stereoisomers" \

search_center = "-12.59711.99021.741"

[tannerjj@europa ligandID]$

Thanks,

Jack

--

John J. Tanner

Professor of Biochemistry and Chemistry

Associate Chair of Biochemistry

Department of Biochemistry

University of Missouri 117 Schweitzer Hall

503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280

Email: [email protected] mailto:[email protected] https://cafnrfaculty.missouri.edu/tannerlab/ https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A

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