Buster/DivCon Usage and Tutorial

Buster/DivCon Usage and Tutorial

We are very excited to announced a new addition to our product line! In recent, developer/beta releases, we demonstrate the availability of the BUSTER/DivCon plugin. This plugin to the BUSTER crystallographic platform from Global Phasing Limited covers all of the same tools and approaches – including XModeScore – as found with our Phenix plugin, but with BUSTER serving as the refinement engine instead of Phenix. Very special thanks to the BUSTER team at Global Phasing for providing much needed feedback and support during this new integration!

The new user of BUSTER/DivCon should first review the tutorials for Phenix/DivCon and XModeScore. As the tool continues to evolve, additional BUSTER-specific tutorials will be provided. But for the most part, the same command line options, tools, and logic applies to use of the DivCon plugin in both platforms. The following general notes apply to the use of BUSTER in place of Phenix:

  • To use the BUSTER plugin, simply use the qbbuster executable script in place of the qbphenix executable script noted in the Phenix/DivCon and XModeScore tutorials. Both scripts call the same, underlying Perl script to manage the particular jobs, but each script will supply a –engine option the an argument of “buster” for qbbuster and “phenix” for qbphenix.
  • Current versions of BUSTER expect that protonation will be identical for all ligands as Global Phasing does not yet supply a way to provide a difference CIF for the same ligand 3-letter code. For this reason, if the MOE Protonate3D tool is used, the 3-letter code of the ligand may be changed during refinement to _01, _02, and so on if the protonation states differ.
  • There is currently a known incompatibility between some MOE-generated CIFs and BUSTER. For this reason, we recommend that you use GRADE, MOGUL, or ELBOW with BUSTER to generate CIF files or supply your own.

The qbbuster Command Line arguments cover various standard functions and features available within the toolbox. The documentation below will provide you with a starting point for X-ray crystallography using QM and QM/MM based methods:

Detailed Tutorials

Tutorial #1 (Running BUSTER/DivCon without the qbbuster wrapper): 2BSM

Beginning with the data available on the RCSB Protein Data Bank PDBid:2BSM page the following calculations were performed.

  1. Source the proper Phenix and DivCon versions (assuming Bash shell):
    source /path/to/BUSTER_snapshot_XXX/setup.sh
    source /path/to/DivConDiscoverySuite/etc/qbenv.sh
  2. In a clean, empty directory, place the 2BSM.pdb (without hydrogens as downloaded from PDB) and 2bsm-sf.cif files for treatment in the next step. Note: that qbbuster can download the PDB and structure factors files automatically using the –pdbID command line option.
  3. Create the file ‘divcon.ini. having the following lines:
    region-selection = /A/BSM/1224// 3 0
    hamiltonian = pm6 amberff14sb
    np = 4
  4. Create the file 2BSM.qm that should contain the following lines:
    NOTE BUSTER_SET QM01 =  ALL
    NOTE BUSTER_QM_CHARGE_01 0
    NOTE BUSTER_QM_MULTIP_01 1
    NOTE BUSTER_QM_WRESTR_01 0.0
    NOTE BUSTER_QM_WRITE_PDB_FOR_HELPER ON
    NOTE BUSTER_QM_MAXDISP 1.0E05
    NOTE BUSTER_QM_HELPER $QBHOME/scripts/BusterQMHelper.sh
    NOTE BUSTER_QM_METHOD PM6
    NOTE BUSTER_QM_WEIGHT 3.0
  5. Run Buster refinement as follows. Note: you will need to protonate the 2BSM.pdb file using a tool of your choice (such as DivCon, MOE, or some other executable) creating a file named 2BSM+H.pdb:
    refine -Gelly 2BSM.qm -p 2BSM+H.pdb -m 2BSM.mtz -l BSM.cif -nbig 2  RunGellySanityCheck=no RunGellyScreen=no -qm_weight 3.0

     

Additional Examples

Tutorial #2 (using qbbuster execution script and Grade & DivCon protonator): 2BSM

Beginning with the data available on the RCSB Protein Data Bank PDBid:2BSM page the following calculations were performed.

  1. Source the proper Phenix and DivCon versions (assuming Bash shell):
    source /path/to/BUSTER_snapshot_XXX/setup.sh
    source /path/to/DivConDiscoverySuite/etc/qbenv.sh
  2. In a clean, empty directory, place the 2BSM.pdb (without hydrogens as downloaded from PDB) and 2bsm-sf.cif files for treatment in the next step. Note: that qbbuster can download the PDB and structure factors files automatically using the –pdbID command line option.
  3. Execute the QM region refinement on 4 processors in PHENIX with the command (phenix.elbow can take several minutes to run).
    /path/to/DivConSuite/bin/qbbuster --pdbFile 2BSM.pdb --sfFile 2BSM.mtz
    --protonation divcon --makeCIF grade --mmMethod amberff14sb --qmMethod pm6
    --qmWeight 5.0 --ncycles 2 --selection "resname BSM" --region-radius 3.0
    --np 4 --dir qmRun
  4. You will see the usual Buster outputs and file structure. The refined pdb/mtz : refine.pdb and refine.mtz will be in the directory qmRun

Explanation of parameters:

  • –protonation divcon : use QuantumBio “built in” algorithm to protonate the structure.
  • –mmMethod amberff14sb and –qmMethod pm6 : set ONIOM QM/MM with SE-QM pm6 and AMBERFF14
  • –selection “resname BSM” : set the center of the QM regions(s) to be the ligand BSM
  • –qmWeight 5.0 : set a weight that Buster uses to scale QM energy/gradients
  • –dir qmRun : run Buster in the directory qmRun
  • –makeCIF grade : use the built-in GRADE-based CIF generator from Global Phasing.

Additional Examples

Tutorial #3 (qbbuster and XModeScore): 1TOW

Beginning with the data available on the RCSB Protein Data Bank PDBid:1TOW page the following calculations were performed.

  1. Source the proper Phenix and DivCon versions (assuming Bash shell):
    source /path/to/BUSTER_snapshot_XXX/setup.sh
    source /path/to/DivConDiscoverySuite/etc/qbenv.sh
  2. In a clean, empty directory, place the 1TOW.pdb (without hydrogens as downloaded from PDB) and 1tow-sf.cif files for treatment in the next step. Note: that qbbuster can download the PDB and structure factors files automatically using the –pdbID command line option.
  3. Execute the QM region refinement on 4 processors in PHENIX with the command (phenix.elbow can take several minutes to run).
    /path/to/DivConSuite/bin/qbbuster --pdbFile 1TOW.pdb --sfFile 1TOW.mtz
    --XModeScore --protonation divcon --makeCIF grade --mmMethod amberff14sb
    --qmMethod pm6 --qmWeight 2.0 --selection "resname CRZ chain A resid 501"
    --region-radius 3.0 --protomers "-1..1" --np 24 --dir XModeScoreRun
  4. You will see the usual Buster outputs and file structure. The refined pdb/mtz : refine.pdb and refine.mtz will be in the directory XModeScoreRun

Explanation of parameters:

  • –XmodeScore : Execute XmodeScore
  • –protonation divcon : use QuantumBio “built in” algorithm to protonate the structure.
  • –resname CRZ –resid 501 –chain A : Selection of the ligand to on which to run XModeScore.
  • –protomers “-1,1” : Generate tautomers for the base state as well as possible tautomers for -1 and +1 protonation states.

Additional Examples

Key Resources