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<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>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<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"><span style="color:#0563C1">Email: tannerjj@missouri.edu</span></a><br>
<a href="https://cafnrfaculty.missouri.edu/tannerlab/"><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>
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