Form 0 0 530 654 200 200 APBS Electrostatics 0 0 0 QWidget[transparent_background=true] {background-color:transparent} QFrame::NoFrame Qt::ScrollBarAlwaysOff true true Main 0 0 485 965 true 10 12 10 10 Selection: input_sele 0 0 true polymer true background: #f66; padding: 5; Selection has ... QFrame::StyledPanel uncheck if the selected molecule already has partial charges and radii ("elec_radius" property) assigned, e.g. if you have loaded a PQR file Prepare Molecule true Qt::Horizontal 40 20 Options >> true true 0 0 QLayout::SetDefaultConstraint 0 0 0 0 Method: prep_method pdb2pqr prepwizard (SCHRODINGER) protein_assign_charges_and_radii use formal_charge and vdw use CB-pseudocharge and vdw use CA-pseudocharge and radius=3.0 use vdw Qt::Horizontal 40 20 prepared Output Molecule Object: prep_name 0 0 0 0 0 0 0 "pdb2pqr" adds hydrogens and missing sidechain atoms, assigns partial charges and radii. REMOVES ligands and modified residues. Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true Ignore warnings 0 0 0 0 0 0 "prepwizard" adds hydrogens and missing sidechain atoms, and assigns partial charges. Can handle ligands and modified residues. PyMOL's vdw radii will be used. Requires Schrodinger Suite. Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true Additional command line options for prepwizard, for example "-r 2.0" or "-fix" extra command line options 0 0 0 0 0 0 "protein_assign_charges_and_radii" REMOVES incomplete or modified residues, adds missing C-terminus, and assigns AMBER99 partial charges and radii Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true 0 0 0 0 0 0 Coarse grained charge model: use formal charges (-1/0/1) and PyMOL's vdw radii. Note that missing sidechains of charged residues (e.g. GLU) will not contribute any charge! Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true 0 0 0 0 0 0 Coarse grained charge model for proteins with "stub" side chains: place a pseudo charge on the CB atom of GLU, ASP, ARG and LYS Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true 0 0 0 0 0 0 Coarse grained charge model for CA-only models: place a pseudo charge on the CA atom of GLU, ASP, ARG and LYS and set a radius of 3.0 for all atoms Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true 0 0 0 0 0 0 Use existing "partial_charge", use vdw as "elec_radius" Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true QFrame::StyledPanel Calculate Map with APBS true Qt::Horizontal 40 20 Options >> true 0 0 0 0 limit the expensive fine grid calculation to a region of interest, e.g. a binding pocket Focus Selection (optional): focus_sele Output Map Object: apbs_map apbs_map Grid spacing not guaranteed, will increase grid spacing if grid doesn't fit into memory Grid Spacing: apbs_grid Angstrom 0.010000000000000 0.250000000000000 0.500000000000000 QFrame::StyledPanel Molecular Surface Visualization true Qt::Horizontal 40 20 Options >> true false 0 0 0 0 Map: surf_map false true Range: +/- surf_range 5.000000000000000 Output Ramp: surf_ramp apbs_ramp Solvent Excluded Surface (Connolly surface) Solvent Accessible Surface true Projects the electrostatic potential onto the molecular surface QFrame::StyledPanel Other Visualizations optbutton_other Qt::Horizontal 40 20 Options >> true false 0 0 0 0 0 true After the map has been calculated, create additional visualizations using the "Action" items in the object menu panel: true Isosurface with "A > surface > level +/-1.0" 10 Volume with "A > volume > esp" 10 Field lines with "A > gradient > default" 10 Slice with "A > slice > default" 10 Qt::Vertical 20 0 APBS Template 10 12 10 10 Documentation: <a href="https://apbs.readthedocs.io/en/latest/using/input/elec/">apbs.readthedocs.io</a> true Load existing "apbs.in" file: Browse... Qt::Horizontal 40 20 Reset Monospace QPlainTextEdit::NoWrap Advanced Configuration 10 12 10 10 Program Locations apbs apbs_exe ... pdb2pqr pdb2pqr_exe ... pdb2pqr command line options: pdb2pqr_args --ff=AMBER For RNA, use residue names RA, RC, RG, RU true Objects and Files Don't group new objects Don't delete temporary files Qt::Vertical 20 40 Register APBS Use Run input_sele do_prepare prep_method prep_name do_apbs focus_sele apbs_grid apbs_map do_surface surf_map surf_range surf_ramp surf_type button_register button_ok tabWidget apbs_exe apbs_exe_browse pdb2pqr_exe pdb2pqr_exe_browse pdb2pqr_args optbutton_surface toggled(bool) optarea_surf setVisible(bool) 484 206 368 261 do_surface toggled(bool) optarea_surf setEnabled(bool) 268 210 269 261 optbutton_apbs toggled(bool) optarea_apbs setVisible(bool) 484 51 320 94 do_apbs toggled(bool) optarea_apbs setEnabled(bool) 229 53 145 94 optbutton_prepare toggled(bool) optarea_prep setVisible(bool) 484 -155 325 -89 do_prepare toggled(bool) optarea_prep setEnabled(bool) 157 -163 128 -90 apbs_map textChanged(QString) surf_map setEditText(QString) 442 163 442 297 do_apbs toggled(bool) surf_map setDisabled(bool) 229 53 442 297 optbutton_other toggled(bool) optarea_other setVisible(bool) 484 435 429 502 prep_method currentIndexChanged(int) stackedWidget setCurrentIndex(int) 401 -119 199 -38