[phenixbb] phenix.ligand_identification search_center

Tanner, John J. TannerJJ at missouri.edu
Wed Mar 31 13:25:07 PDT 2021

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 at 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 = "-12.597  11.990  21.741"

[tannerjj at europa ligandID]$



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: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

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