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 = "-12.597
11.990
21.741"
[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]
https://cafnrfaculty.missouri.edu/tannerlab/
Lab:
Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt
Annex 203A