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<div class="moz-cite-prefix">Hi Jack, <br>
<br>
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.<br>
In your case, you'd use:<br>
<br>
search_target.search_center=<span class="s1">"-12.597</span><span
class="apple-converted-space">
</span><span class="s1">11.990</span><span
class="apple-converted-space"> </span>
<span class="s1">21.741"<br>
search_parameters.number_of_ligands=6<br>
<br>
The rest will remain the same.<br>
I'll update the documentation to make it clearer. Feel free to
email me with any questions.<br>
<br>
Best,<br>
<br>
Li-Wei<br>
</span><br>
<br>
On 3/31/2021 1:25 PM, Tanner, John J. wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BN6PR01MB2772A8C9E1A2B405ED1DEC98A77C9@BN6PR01MB2772.prod.exchangelabs.com">
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<div class="WordSection1">
<p class="MsoNormal">Phenix BB:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span class="s1">[tannerjj@europa ligandID]$ cat
ligandID.com</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">phenix.ligand_identification \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">mtz_in =
"/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.mtz" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">mtz_type = diffmap \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">input_labels = "FOFCWT PHFOFCWT" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">ligand_list = "DPR PRO HYP HZP UYA UY7" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">model =
"/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.pdb" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">ncpu = 4 \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">output_dir =
"/titan/tanner/MmP5CDH/THLP/ligandID/temp" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">number_of_ligands = 6 \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">job_title = "THLP8-1_003 D,L-Pro and 4 OH-Pro
stereoisomers" \</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">search_center = "-12.597</span><span
class="apple-converted-space">
</span><span class="s1">11.990</span><span
class="apple-converted-space"> </span>
<span class="s1">21.741"</span><o:p></o:p></p>
<p class="p1"><span class="s1">[tannerjj@europa ligandID]$</span><span
class="apple-converted-space"> </span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Jack <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">-- <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">John
J. Tanner <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">Professor
of Biochemistry and Chemistry<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">Associate
Chair of Biochemistry<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">Department
of Biochemistry<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">University
of Missouri<br>
117 Schweitzer Hall<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">503
S College Avenue<br>
Columbia, MO 65211<br>
Phone: 573-884-1280<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black"><a
href="mailto:tannerjj@missouri.edu" target="_blank"
moz-do-not-send="true"><span style="color:#0563C1">Email: tannerjj@missouri.edu</span></a><br>
<a href="https://cafnrfaculty.missouri.edu/tannerlab/"
moz-do-not-send="true"><span style="color:#0563C1">https://cafnrfaculty.missouri.edu/tannerlab/</span></a><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:11.5pt;font-family:Helvetica;color:black">Lab:
Schlundt Annex rooms 3,6,9, 203B, 203C<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.5pt;font-family:Helvetica;color:black;background:white">Office: Schlundt
Annex 203A</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
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