[phenixbb] phenix.ligand_identification search_center

Li-Wei Hung lwhung at lbl.gov
Wed Mar 31 15:05:06 PDT 2021


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 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 = "-12.59711.99021.741"
>
> [tannerjj at 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: tannerjj at missouri.edu <mailto:tannerjj at missouri.edu>
> 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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