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For background to commands see Intermediate Tutorial and the BUSTER reference card |
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fetch PDB entry 2h7p and its structure factors, converting the SF to mtz with checks
fetch_PDB 2h7p >& fetch_PDB_2h7p_log.txt
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create a grade restraint dictionary for the ligand
grade_PDB_ligand 468
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add hydrogen atoms to both protein and ligand using MolProbity reduce
hydrogenate -p 2h7p/2h7p.pdb -o 2h7p_hydrogenate.pdb -l 468.grade_PDB_ligand.cif
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perform a BUSTER MapOnly run to get maps. Include buster-report
refine -p 2h7p_hydrogenate.pdb -m 2h7p/2h7p.mtz -l 468.grade_PDB_ligand.cif -M MapOnly -d 00_MapOnly -report >& 00_MapOnly_log.txt
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do a full reciprocal space refinement to adjust protein and ligand
refine -p 2h7p_hydrogenate.pdb -m 2h7p/2h7p.mtz -l 468.grade_PDB_ligand.cif -M TLSbasic -d 01_refine -report >& 01_refine_log.txt
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linux command to strip out the ligand from the refined coordinates
grep -v "468 A 501" 01_refine.report/01_refine.report.pdb > 01_refine_noA468.pdb
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do a MapOnly run on "apo" protein to get ligand difference density to show process of fitting clear initial difference map.
refine -p 01_refine_noA468.pdb -m 2h7p/2h7p.mtz -l 468.grade_PDB_ligand.cif -M MapOnly -d 02_apo_MapOnly >& 02_apo_MapOnly_log.txt