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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