True Coot GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 0 0.5 GTK_SHADOW_ETCHED_IN 0 False False True False 0 True GTK_PACK_DIRECTION_LTR GTK_PACK_DIRECTION_LTR True _File True True pdb, cif or shelx res format Open Coordinates... True True gtk-open 1 0.5 0.5 0 0 True Auto Open MTZ... True True gtk-open 1 0.5 0.5 0 0 True Create a map "on the fly" from mtz, phs or mmCIF data Open MTZ, mmCIF, fcf or phs... True True gtk-open 1 0.5 0.5 0 0 True Open a pre-calculated CCP4 map Open Map... True True gtk-open 1 0.5 0.5 0 0 True Close molecule/map... True True gtk-close 1 0.5 0.5 0 0 True Import CIF dictionary... True True gtk-add 1 0.5 0.5 0 0 True Give a 3-letter code and use libcheck to generate coordinates from REFMAC monomer library Get Monomer... True True connect-to-ccp4.svg 0.5 0.5 0 0 True Search monomer names to find 3-letter code Search Monomer Library... True True gtk-index 1 0.5 0.5 0 0 True SMILES... True True smiles.png 0.5 0.5 0 0 True Get PDB Coordinates file from server using accession code Get PDB using Accession Code... True True connect-to-oca.svg 0.5 0.5 0 0 True Use the Electron Density Server at Uppsala University to get coords and map... (Long live the EDS!) Get PDB & Map using EDS... True True connect-to-usf.svg 0.5 0.5 0 0 True Save Coordinates... True True gtk-save 1 0.5 0.5 0 0 True Save Symmetry Coordinates... True True coot-save-symm.png 0.5 0.5 0 0 True Save State... True True coot-save.png 0.5 0.5 0 0 True Recover Session... True True gtk-find-and-replace 1 0.5 0.5 0 0 True bye Exit True True gtk-quit 1 0.5 0.5 0 0 True _Edit True True Map Colour... True True gtk-select-color 1 0.5 0.5 0 0 True Map Parameters... True True gtk-preferences 1 0.5 0.5 0 0 True Bond Colours... True True gtk-select-color 1 0.5 0.5 0 0 True Bond Parameters... True True gtk-preferences 1 0.5 0.5 0 0 True Restraints... True True radacina_handcuffs-small.svg 0.5 0.5 0 0 True Skeleton Parameters True True gtk-preferences 1 0.5 0.5 0 0 True Skeleton Colour... True True gtk-select-color 1 0.5 0.5 0 0 True Skeleton Box Radius... True True Skeletonization Level... True True Residue Info... True True residue-info.png 0.5 0.5 0 0 Font Size... True True gtk-font.png 0.5 0.5 0 0 Pink Pointer Size... True True pink-pointer.png 0.5 0.5 0 0 True Background Colour... True True gtk-select-color 1 0.5 0.5 0 0 True Black True True True White True True background_black1 True Preferences... True True gtk-preferences 1 0.5 0.5 0 0 True _Calculate True True Model/Fit/Refine... True True gtk-find-and-replace 1 0.5 0.5 0 0 True Other Modelling Tools... True True gnome-run.png 0.5 0.5 0 0 True SSM Superpose... True True Least squares fit structures using residue range LSQ Superpose... True True Merge Molecules... True True merge-molecules.svg 0.5 0.5 0 0 True Mutate Residue Range... True True Align & Mutate... True True Renumber Residues... True True renumber-residues.svg 0.5 0.5 0 0 True Change Chain IDs... True True change-chain-id.svg 0.5 0.5 0 0 True Move Molecule Here... True True Fit Loop... True True Map Sharpening... True True Map Skeleton... True True NCS Maps... True True calculate-ghosts.svg 0.5 0.5 0 0 True Frames/Sec... True True appointment-new.png 0.5 0.5 0 0 True Scripting... True True gtk-justify-left 1 0.5 0.5 0 0 True Python... True True Scheme... True True Run Script... True True gtk-execute 1 0.5 0.5 0 0 True _Draw True True Go To Atom... True True gtk-jump-to 1 0.5 0.5 0 0 True Control display and activity of maps and molecules Display Manager... True True display-manager.png 0.5 0.5 0 0 True Undo Last Navigation True True gtk-undo 1 0.5 0.5 0 0 True Centre Atom Label... True True gtk-justify-center 1 0.5 0.5 0 0 True Sequence View True True sequence-view.png 0.5 0.5 0 0 True Anisotropic Atoms... True True aniso-atom.png 0.5 0.5 0 0 True Cell & Symmetry... True True cell+symm.png 0.5 0.5 0 0 True Additional Representation... True True Non-crystallographic Ghost Controller NCS Ghost Control... True True ghosts.png 0.5 0.5 0 0 True Spin View On/Off True True spin-view.png 0.5 0.5 0 0 True Screenshot True True panel-screenshot.png 0.5 0.5 0 0 True Simple... True True Povray... True True Raster3D... True True Generic Display Objects... True True generic-display-objects.svg 0.5 0.5 0 0 Antialiasing... True True add-peptide-1.svg 0.5 0.5 0 0 True Stereo... True True stereo-view.svg 0.5 0.5 0 0 True Clipping... True True Crosshairs... True True crosshairs.png 0.5 0.5 0 0 True Zoom... True True gtk-zoom-in 1 0.5 0.5 0 0 Dragged Map... True Smooth Recentring... True Coordinates Recentring... True True _Measures True True Display atom names, temperature factors and occupances of all atoms in the residue Residue Info... True True residue-info.png 0.5 0.5 0 0 True Distances & Angles... True True gtk-unindent 1 0.5 0.5 0 0 True Environment Distances... True True env-distances.png 0.5 0.5 0 0 True Plane Distances... True True plane-distances.png 0.5 0.5 0 0 True Pointer Distances... True True pointer-distances.png 0.5 0.5 0 0 True Clear Atom Labels True True gtk-clear 1 0.5 0.5 0 0 True _Validate True True Ramachandran Plot True True ramachandran.png 0.5 0.5 0 0 True Ramachandran Difference Plot Kleywegt Plot... True True kleywegt.svg 0.5 0.5 0 0 True Incorrect Chiral Volumes... True True chiral.png 0.5 0.5 0 0 True Unmodelled blobs... True True unknown-blob.svg 0.5 0.5 0 0 True Difference Map Peaks... True True diff-map.svg 0.5 0.5 0 0 True Check/Delete Waters... True True water-drop.svg 0.5 0.5 0 0 True Check waters by Difference Map Variance... True True water-diff-map.svg 0.5 0.5 0 0 True Flags distortions in Bond, Angles and Planes Geometry analysis True True geom.svg 0.5 0.5 0 0 True Flags deviations from Trans Peptide Peptide omega analysis True True peptide-omega.svg 0.5 0.5 0 0 True Flags Residues with Large Variance in Atom B factors Temp. fact. variance analysis True True temperature.svg 0.5 0.5 0 0 True Nakagawa's Bees (probable flips): identify OE1 and NE2 B-factor outliers in GLNs (similarly ASNs are analysed) GLN and ASN B-factor Outliers True True gln-asn-b-factors.svg 0.5 0.5 0 0 True Flags Unusual Rotamers, Missing Atoms and Nomenclature Errors Rotamer analysis True True rotamers.svg 0.5 0.5 0 0 True Density fit analysis True True density-fit.svg 0.5 0.5 0 0 True Probe clashes True True probe-clash.svg 0.5 0.5 0 0 True NCS Differences True True HID True True Recentre of the last read molecule that is displayed Reset View True True gtk-zoom-fit 1 0.5 0.5 0 0 True ScrollWheel True True scroll-wheel.svg 0.5 0.5 0 0 True Attach scroll wheel to which map? True Virtual Trackball True True Flat True True True Spherical Surface True True flat1 True About True True On Line Docs URL... True True gtk-justify-fill 1 0.5 0.5 0 0 True About... True True gtk-about 1 0.5 0.5 0 0 True Hints... True True gtk-dialog-info 1 0.5 0.5 0 0 0 False False True GTK_ORIENTATION_HORIZONTAL GTK_TOOLBAR_BOTH_HORIZ True False True Usage Note: click again to centre on a different molecule Reset View True gtk-zoom-fit True True True False True True Display the dialog for displaying and undisplaying molecules and changing their representation Display Manager True display-manager.png True True True False True True True True False True True 6 True GTK_RELIEF_NORMAL False True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-stop 4 0.5 0.5 0 0 0 False False True Stop True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True True GTK_RELIEF_NORMAL False True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-apply 4 0.5 0.5 0 0 0 False False True Continue True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True False True GTK_RELIEF_NORMAL False True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False False False 0 False False 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 2 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 0 0.5 GTK_SHADOW_NONE True False 0 True False True GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True 1 8 False 0 0 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Chirals True False 4 5 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Bonds True False 0 1 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Angles True False 1 2 0 1 fill 2 34 20 0.019999999553 0.5 GTK_SHADOW_ETCHED_OUT True Torsions True False 2 3 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Planes True False 3 4 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True WARNING:: CIS peptides True False 7 8 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Non-bonded Contacts True False 5 6 0 1 fill 2 34 20 0 0.5 GTK_SHADOW_ETCHED_OUT True Ramachandran Plot deviance True False 6 7 0 1 fill 0 True True 0 True True 0 True True 1 GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-refresh 4 0.5 0.5 0 0 0 False False True Reverse True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False 1 True GTK_BUTTONBOX_END 0 True False 0 True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True Accept True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Reject True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 True True 0 True True 0 False True True 0 0 GTK_SHADOW_NONE True True 0 0 True True True True 0 False False 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True GTK_SHADOW_NONE GTK_POS_TOP GTK_POS_RIGHT 3 True GTK_ORIENTATION_VERTICAL GTK_TOOLBAR_ICONS True False True True True False True Refine/Regularize Control... True R/RC True GTK_RELIEF_NORMAL False False False True True True False True Select Map... True Map True GTK_RELIEF_NORMAL False False False True Real Space Refine Zone Real Space Refine Zone True refine-1.svg True True True False False True True Send in the Bond Angels! Ahem, I mean "Regularize Zone (click 2 atoms)" Regularize Zone True regularize-1.svg True True True False False True True Fix Atoms in Refinement and Regularization... Fixed Atoms... True anchor.svg True True False False True True Rigid Body Fit Zone (click on 2 atoms) Rigid Body Fit Zone True rigid-body.svg True True False False False True True Rotate Translate True rtz.svg True True False False False True Auto Fit Rotamer (click on an atom) Auto Fit Rotamer True auto-fit-rotamer.svg True True False False False True True Rotamers... (click on an atom) Rotamers... True rotamers.svg True True False False False True True Edit Chi Angles (click on an atom) Edit Chi Angles True edit-chi.svg True True False False False True True Torsion General Torsion General True torsion-general.svg True True False False False True True Flip peptide... (click on an atom) Flip Peptide True flip-peptide.svg True True False False False True True Flip sidechain 180 degrees (click on an atom) Sidechain 180 Degree Flip True side-chain-180.svg True True False False False True True Change Residue's Phi and Psi Edit Backbone Torsions True edit-backbone.svg True True False False False True True True True False 13 True False False True True False True False False True Mutate & AutoFit... (click on an atom) Mutate & Auto Fit... True mutate-auto-fit.svg True True False False False True True Simple Mutate (mutates amino acid residues and nucleic acids) A simple modelling tool - no map fitting happens Simple Mutate... True mutate.svg True True False False False True Solvate... Find Waters... True add-water.svg True True True False True True Add Residue... Add Terminal Residue... True add-peptide-1.svg True True False False False True True Add Alternate (Alternative) Conformation to a Residue Add Alt Conf... True add-alt-conf.svg True True True False True True Place Atom at Pointer... Place Atom At Pointer True atom-at-pointer.svg True True False False True True Clear Pending Picks Clear Pending Picks True gtk-clear True True False False True True Delete Item... Delete... True gtk-delete True True False False True True Undo Undo True gtk-undo True True False False True True Redo Redo True gtk-redo True True False False True True True True False 13 True False False True True False True False False True Press to run Refmac Run Refmac... True azerbaijan.svg True True False False True True True True False 15 True False False True True True False True 0.5 0.5 1 1 0 0 0 0 True Use this to change between text, icons or both GTK_PACK_DIRECTION_LTR GTK_PACK_DIRECTION_LTR True True True gtk-media-play 1 0.5 0.5 0 0 True Icons True False True Icons and text True False model_toolbar_icons1 True Text True True model_toolbar_icons1 True True Main Icons True False True All Icons True True model_toolbar_main_icons True User defined True False model_toolbar_main_icons False False 0 False False 0 0.5 GTK_SHADOW_ETCHED_IN 0 True True 10 True Select Coordinates File GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True True True GTK_RELIEF_NORMAL True True True True GTK_RELIEF_NORMAL True 10 True Select Dataset File GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True True True GTK_RELIEF_NORMAL True True True True GTK_RELIEF_NORMAL True True Column Label Assignment GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False 6 True False 0 True False 0 True False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True When clicked, add anomalous and resolution limit options (generally not needed) True Expert Mode? True GTK_RELIEF_NORMAL True 0 False False 0 True True True Column Labels for Map Synthesis: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 7 False False True False 0 True 0 0.5 GTK_SHADOW_ETCHED_IN 5 True False 0 True Amplitudes False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 3 False False True True -1 0 False False 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN 5 True False 0 True Phases False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 3 False False True True -1 0 False False 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True False 0 True False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 4 True Weights are usually used for experimental phasing. When making a map from REFMAC output one (almost) never needs Weights. True Use Weights? True GTK_RELIEF_NORMAL True False False True 0 False False 0 True True 6 True False False 0 True Weights False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 3 False False True Usually not needed for map from refmac... True -1 0 False False 0 True True 0 True True 3 0 0.5 GTK_SHADOW_ETCHED_IN 10 True False 0 True True Use Resolution Limits True GTK_RELIEF_NORMAL True False False True 0 False False True False False 0 True Low: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True True True 0 True * False 0 False False True False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True High: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True True True 0 True * False 0 False False 0 True True True Resolution limits False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True True See Section 6.5 of the User Manual for default Diference Map colouring. True Is a Difference Map True GTK_RELIEF_NORMAL True False False True 7 False False True 10 True True True If you want to use these data to run refmac, you will need to assign the columns for the observations, the sigmas thereof and the R free... True Assign Labels for Refmac? True GTK_RELIEF_NORMAL True False False True 0 False False True False 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True False 26 True Fobs False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True -1 0 False False 2 True True True False 4 True Sig Fobs False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True -1 0 False False 2 True True True False 21 True R free False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True -1 0 False False 2 True True 0 True True 0 True True 2 True False 0 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 6 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 6 True True 11 True True True (Thinking, not crashing) False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True Clipping Window GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Clipping Adjustment False False GTK_JUSTIFY_CENTER False False 0 7.45058015283e-09 5 5 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 9 True 0 0.5 GTK_SHADOW_ETCHED_IN True True True GTK_POS_TOP 1 GTK_UPDATE_CONTINUOUS False 0 0 0 0 0 0 8 True True 6 True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False True Global map properties window GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Density Settings False False GTK_JUSTIFY_CENTER False False 0.5 0.5 2 6 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Map Radius: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 7 False False True True True True 0 True * False 11 False True True Angstroems False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 18 False False True True Apply True GTK_RELIEF_NORMAL True 0 False False True False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Increment Size False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True True True True 0 True * False 6 False True True e/A^3 False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Diff Map Increment False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True True True True 0 True * False 0 False True True e/A^3 False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 True True 6 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Sampling Rate: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True Shannon Sampling multiplier. 1.5 is the standard value. Use larger numbers for smoother maps True True True 0 True * False 0 False True 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 1 True True Dynamic Map Sampling True GTK_RELIEF_NORMAL True False False True 0 False False True True Dynamic Map Display Size True GTK_RELIEF_NORMAL True False False True 0 False False 0 True True True 6 True True 10 True False 0 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 10 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 10 True True 0 True True True fps_window GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Show Frames Per Second? False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 5 PANGO_ELLIPSIZE_NONE -1 False 0 4 False False 6 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True True False True radiobutton1 0 False False 0 True True 8 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 6 False False True Active Map on Dragging? GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Active Map on Dragging? False False GTK_JUSTIFY_CENTER False False 0.5 0.5 4 5 PANGO_ELLIPSIZE_NONE -1 False 0 9 False False 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True False False True active_map_radiobutton_yes 0 False False 0 True True 10 True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 9 False False True Show Symmetry? GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Symmetry & Unit Cell False False GTK_JUSTIFY_CENTER False False 0.5 0.5 3 5 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 6 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 4 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True True False True show_symmetry_yes_radiobutton 0 False False True Master Switch: Show Symmetry Atoms? False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True 4 True True Symmetry by Molecule... True GTK_RELIEF_NORMAL True 4 False False 4 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Symmetry Atom Display Radius: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 12 2 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True False 0 True Radius: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True True True 0 True * False 0 True True True A False False GTK_JUSTIFY_CENTER False False 0.5 0.5 5 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 0 True True 4 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True False 0 True Symmetry Colour False False GTK_JUSTIFY_CENTER False False 0.5 0.5 10 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True GTK_RELIEF_NORMAL True True False 0 True 0 0.5 GTK_SHADOW_ETCHED_IN True True False True 0 True True True Sym Colour False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 2 False False 4 False False 6 True True True False 0 4 True 0 0.5 GTK_SHADOW_ETCHED_IN 4 True False 0 True Colour Merge: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 4 False False True True True GTK_POS_TOP 1 GTK_UPDATE_CONTINUOUS False 0 0 0 0 0 0 0 True True 0 True True 0 True True 0 True True True True Expanded Symmetry Atom Labels? True GTK_RELIEF_NORMAL True False False True 0 False False True Symmetry False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True True False True unit_cell_yes_radiobutton 0 False False True Show Unit Cells? False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True True False 0 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-apply 4 0.5 0.5 0 0 0 False False True Apply True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 4 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 4 True True 9 False False True About... GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 220 174 True GTK_POLICY_NEVER GTK_POLICY_ALWAYS GTK_SHADOW_IN GTK_CORNER_TOP_LEFT True True False False True GTK_JUSTIFY_LEFT GTK_WRAP_WORD True 0 0 0 0 0 0 0 True True True False 0 8 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True False 8 True True Other... True GTK_RELIEF_NORMAL True 0 True False 0 False False True Anisotripic Atoms GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Show Anisotropic Atoms? False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True False False True show_aniso_yes_radiobutton 0 False False 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Limit Display Radius of Anisotropic Atoms? False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 2 False False 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True False False True limit_display_radius_yes_radiobutton 0 False False 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Display Limit Radius False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 5 True False 0 True True True True 0 True * False 3 True True True A False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 3 False False 0 True True 0 True True 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Probability False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 2 False False True False 0 True True True GTK_POS_TOP 1 GTK_UPDATE_CONTINUOUS False 0 0 0 0 0 0 6 True True True % False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 3 False False 0 True True 0 True True 0 True True 2 True True 0 4 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True Appy True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False 4 True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-close 4 0.5 0.5 0 0 0 False False True Close True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False 1 False False True window2 GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Recentring Smooth Scrolling False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False True False 0 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Yes True GTK_RELIEF_NORMAL True False False True 0 False False True True No True GTK_RELIEF_NORMAL True False False True smooth_scroll_yes_radiobutton 0 False False 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Number of Steps: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 10 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False True True True True 0 True * False 10 True True 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Do Not Scroll for distances more than: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 4 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False True True True True 0 True * False 7 True True True A False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False 0 True True 0 True True 5 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False False True window2 GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Atom Label Font Size False False GTK_JUSTIFY_CENTER False False 0.5 0.5 4 2 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Small True GTK_RELIEF_NORMAL True False False True 0 False False True True Medium True GTK_RELIEF_NORMAL True False False True font_size_small_radiobutton 0 False False True True Large True GTK_RELIEF_NORMAL True False False True font_size_small_radiobutton 0 False False 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 10 True Select Map... GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True True True GTK_RELIEF_NORMAL True True True True GTK_RELIEF_NORMAL True True .phs Info GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True .phs files additionally need cell and symmetry. We need a pdb file to assign them. (Note that this will not read coordinates - just the cell and symmetry) False False GTK_JUSTIFY_CENTER False False 0.5 0.5 5 5 PANGO_ELLIPSIZE_NONE -1 False 0 2 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 6 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 5 True True 6 True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 5 True True 0 True True 10 True Select Coordinates File for .phs symm/cell GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True True True GTK_RELIEF_NORMAL True True True True GTK_RELIEF_NORMAL True 500 316 True Display Manager GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False 4 True False 0 True True True False 0 2 True False 0 True Maps False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True All True GTK_RELIEF_NORMAL True True False 0 False False 0 False False True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN True False 0 0 True True True True True False 0 2 True False 0 True Molecules False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True All True GTK_RELIEF_NORMAL True True False 0 False False 0 False False True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN True False 0 0 True True True True 0 True True 2 True True True True True 0 0.5 GTK_SHADOW_ETCHED_IN True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-close 4 0.5 0.5 0 0 0 False False True Close True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 False True True Go To Atom... GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True Define an Atom for Centering: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 6 5 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True False 0 3 True False 0 2 True True -1 0 False False True Molecule False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 False True 2 True 3 2 False 0 0 True True Update from Current Postion True GTK_RELIEF_NORMAL True 1 2 0 1 2 160 True False 0 50 True True True True 0 True * False 0 False True True Atom Name False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 1 2 3 2 160 True False 0 50 True True True True 0 True * False 0 False True True Residue Number False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 1 1 2 2 140 True False 0 50 True True True True 0 True * False 0 False False True Chain False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 1 0 1 0 True True 0 False True 0 False True True 0 False True True True 0 6 True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-media-previous 4 0.5 0.5 0 0 0 False False True Previous Residue True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 6 True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-media-next 4 0.5 0.5 0 0 0 False False True Next Residue True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 0 False False 6 179 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT 0 True True True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT 0 True True 0 True True True False 0 3 True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-apply 4 0.5 0.5 0 0 0 False False True Apply True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 5 True True 3 True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-close 4 0.5 0.5 0 0 0 False False True Close True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 6 True True 0 False True True Skeleton Box Size GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Skeleton Box Size False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 8 False False True False 0 True Size False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 4 False False True True True True 0 True * False 0 False True True Angstoms False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 6 True True 6 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 4 True True True True OK True GTK_RELIEF_NORMAL True 0 True True 4 True True True Cancel True GTK_RELIEF_NORMAL True 0 True True 0 True True True Skeletonization Level GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Skeletonization Level False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True False 0 True Level False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True True True True 0 True * False 0 False True True electrons/A^3 False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 0 True True 6 True False 0 True True True True OK True GTK_RELIEF_NORMAL True 0 True True True True True Apply True GTK_RELIEF_NORMAL True 0 True True True True True Cancel True GTK_RELIEF_NORMAL True 0 True True 0 True True True window2 GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Rotation Centre Cube Size False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False True False 0 True Size: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 7 False False True True True True 0 True * False 0 True True True Angstroems False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False 2 True True 6 True True True True True OK True GTK_RELIEF_NORMAL True 0 True True True Choose Cell for PHS file: GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False 290 126 True False 0 True Choose a Symmetry and Cell for the Phases file False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 6 False False True False 0 0 True True 6 True False 0 True True True True OK True GTK_RELIEF_NORMAL True 0 True True True True True Cancel True GTK_RELIEF_NORMAL True 0 True True 0 True True True PDB Accession Code GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False 7 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True PDB Accession Code: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True False 0 True True True True 0 True * False 2 True True 2 True True Get it True GTK_RELIEF_NORMAL True 0 False False 2 False False 2 True Dynarama GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True Ramachandran Plot False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 2 False False True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN 0 True True 6 True 0 0.5 GTK_SHADOW_ETCHED_IN 4 True False 0 True In Prefered Regions: 239 (85.02%) False False GTK_JUSTIFY_CENTER False False 0 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True In Allowed Regions: 365 (23.45%) False False GTK_JUSTIFY_CENTER False False 0 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True Outliers: 34 (0.23%) False False GTK_JUSTIFY_CENTER False False 0 0.5 6 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 False False True False 0 6 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True OK True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 6 True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 0 True True 0 False False True Properies GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True True True True GTK_POS_TOP False False True False 0 True True Labels True GTK_RELIEF_NORMAL True True False True 0 False False True True Sticky Labels True GTK_RELIEF_NORMAL True True False True 0 False False False True True Labels False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 tab 0 True True True 0 True True True True True True OK True GTK_RELIEF_NORMAL True 0 False False 10 True window2 GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_NORMAL GDK_GRAVITY_NORTH_WEST True False True False 0 True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_IN GTK_CORNER_TOP_LEFT True True False False True GTK_JUSTIFY_LEFT GTK_WRAP_WORD True 0 0 0 0 0 0 0 True True True True True True 0 True * False 5 False False 2 True Find Ligands GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True False 0 True GTK_BUTTONBOX_END True True 0 True False 0 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-ok 4 0.5 0.5 0 0 0 False False True Find 'em! True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 True True True True True GTK_RELIEF_NORMAL True True 0.5 0.5 0 0 0 0 0 0 True False 2 True gtk-cancel 4 0.5 0.5 0 0 0 False False True Cancel True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False 2 True True 0 True True 0 False True GTK_PACK_END True False 0 5 True False 0 True Select Map: False False GTK_JUSTIFY_LEFT False False 0.5 0.5 5 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True 0 0.5 GTK_SHADOW_ETCHED_IN True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN True False 0 0 True True 0 False True 5 True False 0 True Select Protein (Masks Map): False False GTK_JUSTIFY_CENTER False False 0.5 0.5 5 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True 0 0.5 GTK_SHADOW_ETCHED_IN True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN True False 0 0 True True 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True Treat waters like protein (mask) atoms True GTK_RELIEF_NORMAL True False False True 0 False False True True Ignore waters for mask True GTK_RELIEF_NORMAL True False False True find_ligand_mask_waters_yes_radiobutton 0 False False True Mask Waters? False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 False False 5 True False 0 True Select Ligands to Search for: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 5 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True 0 0.5 GTK_SHADOW_ETCHED_IN True GTK_POLICY_ALWAYS GTK_POLICY_ALWAYS GTK_SHADOW_NONE GTK_CORNER_TOP_LEFT True GTK_SHADOW_IN True False 0 0 True True 0 True True True 0 0.5 GTK_SHADOW_ETCHED_IN True 0.5 0.5 1 1 0 0 12 0 True False 0 True True Everywhere True GTK_RELIEF_NORMAL True True False True 0 False False True True Right here True GTK_RELIEF_NORMAL True False False True find_ligands_search_all_radiobutton 0 False False True Where to Search? False True GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True 5 True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True True True True 0 True * False 0 False True True sigma False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True Sigma Level False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 False False True 0 0.5 GTK_SHADOW_ETCHED_IN True False 0 True False 0 True Number of Conformers to Search: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True True True 0 True * False 0 False False 0 True True True False 0 True Search Number of Top Sites: False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 False False True True True True 0 True * False 0 False False 0 True True True Expert Options False False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 label_item 0 True True 0 True True True May Atoms in Ligand Check GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True False 0 True GTK_BUTTONBOX_END True False 0 2 True True Continue True GTK_RELIEF_NORMAL True 6 True True 2 True True Cancel True GTK_RELIEF_NORMAL True 6 True True 0 False True GTK_PACK_END 6 True 0 0.5 GTK_SHADOW_ETCHED_IN True One or more of the selected ligands has unexpectedly many atoms. This is an opportunity for you to reflect on that... Do you want to continue? False False GTK_JUSTIFY_CENTER False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 5 False False True Model/Fit/Refine GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE False True False True False False GDK_WINDOW_TYPE_HINT_DIALOG GDK_GRAVITY_NORTH_WEST True False True True False 0 True GTK_BUTTONBOX_END True True True True True Close True GTK_RELIEF_NORMAL True 0 0 False False GTK_PACK_END True 0 0.5 GTK_SHADOW_ETCHED_IN 6 True False 0 1 True Set Parameters for fitting, refinement, regularization, etc. True Refine/Regularize Control... True GTK_RELIEF_NORMAL True 0 False False 1 True Select the map that will be used for refinement, rigid body refinement, terminal residue fit and autofitting True Select Map... True GTK_RELIEF_NORMAL True 0 False False True 3 False False 1 True Real Space Refinement: Improve geometry and fit to map True GTK_RELIEF_NORMAL True False False True False 2 True refine-1.svg 0.5 0.5 0 0 0 False False True Real Space Refine Zone True False GTK_JUSTIFY_RIGHT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Idealize model geometry True GTK_RELIEF_NORMAL True False False True False 2 True regularize-1.svg 0.5 0.5 0 0 0 False False True Regularize Zone True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Fix Atoms in Refinement and Regularization... True GTK_RELIEF_NORMAL True True False 2 True anchor.svg 0.5 0.5 0 0 0 False False True Fix Atoms... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Rearrange to find the name of a popular health club True GTK_RELIEF_NORMAL True False False True False 2 True rigid-body.svg 0.5 0.5 0 0 0 False False True Rigid Body Fit Zone True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False True False 0 1 True Click and Drag across the rotation/translation buttons. Use Ctrl-click to move a single atom [but make sure that you have graphics window focus!] True GTK_RELIEF_NORMAL True False False True False 2 True rtz.svg 0.5 0.5 0 0 0 False False True Rotate/Translate Zone True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 True True 1 True GTK_PACK_DIRECTION_LTR GTK_PACK_DIRECTION_LTR True True True gtk-media-play 1 0.5 0.5 0 0 True By Residue Range... True False True By Chain... True False model_refine_dialog_rot_trans_by_residue_range True By Molecule... True False model_refine_dialog_rot_trans_by_residue_range 0 False True 0 True True 1 Click and Drag across the rotation/translation buttons. Use Ctrl-click to move a single atom [but make sure that you have graphics window focus!] True GTK_RELIEF_NORMAL True False False True False 2 True rtz.svg 0.5 0.5 0 0 0 False False True Rotate/Translate Zone True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Click on an atom in a residue to find the best fit rotamer True GTK_RELIEF_NORMAL True False False True False 2 True auto-fit-rotamer.svg 0.5 0.5 0 0 0 False False True Auto Fit Rotamer True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Select Different Conformations for a Residue Sidechan True GTK_RELIEF_NORMAL True False False True False 2 True rotamers.svg 0.5 0.5 0 0 0 False False True Rotamers... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True False 0 False False 1 True Edit the Chi angles (torsions) of an amino acid residue "by hand" (by mouse, that is) True GTK_RELIEF_NORMAL True False False True False 2 True edit-chi.svg 0.5 0.5 0 0 0 False False True Edit Chi Angles True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Named after the famous function in O that Coot users have been having to do without for years (and quite happily too, if (only?) they have had proper dictionaries for their ligands). But it turns out that some users don't have proper dictionaries and they shout loud and often (and at *me* rather than the author of the dictionary generating program would you believe!) So my arm has been twisted eventually (but I resisted for quite a good while, I think)... Enjoy.... (if you must). GTK_RELIEF_NORMAL True False False True False 2 True torsion-general.svg 0.5 0.5 0 0 0 False False True Torsion General True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Peptide flip True GTK_RELIEF_NORMAL True False False True False 2 True flip-peptide.svg 0.5 0.5 0 0 0 False False True Flip Peptide True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Flip the last chi angle of the sidechain by 180 degrees True GTK_RELIEF_NORMAL True False False True False 2 True side-chain-180.svg 0.5 0.5 0 0 0 False False True Sidechain 180 Degree Flip True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Edit Phi/Psi... True GTK_RELIEF_NORMAL True False False 0 False False 1 True Change Residue's Phi and Psi True GTK_RELIEF_NORMAL True False False True False 2 True edit-backbone.svg 0.5 0.5 0 0 0 False False True Edit Backbone Torsions True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False True 3 False False 1 True Where "Fit" means fit to the Selected Map True GTK_RELIEF_NORMAL True False False True False 2 True mutate-auto-fit.svg 0.5 0.5 0 0 0 False False True Mutate & Auto Fit... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Mutate amino acid residues or nucleotides [no crystallographic map fitting is happens] True GTK_RELIEF_NORMAL True False False True False 2 True mutate.svg 0.5 0.5 0 0 0 False False True Simple Mutate... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True [You need a map to do this] Create a new residue at the C or N terminus. The angles are selected at random sample from the phi/psi probability distribution (then fitted to the map), so if at first you don't succeed, give it another bash... True GTK_RELIEF_NORMAL True False False True False 2 True add-peptide-1.svg 0.5 0.5 0 0 0 False False True Add Terminal Residue... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Add Alternate (Alternative) Conformation to a Residue True GTK_RELIEF_NORMAL True True False 2 True add-alt-conf.svg 0.5 0.5 0 0 0 False False True Add Alt Conf... True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False 1 True Put an atom at current pink pointer position True GTK_RELIEF_NORMAL True True False 2 True atom-at-pointer.svg 0.5 0.5 0 0 0 False False True Place Atom At Pointer True False GTK_JUSTIFY_LEFT False False 0.5 0.5 0 0 PANGO_ELLIPSIZE_NONE -1 False 0 0 True True 0 False False True 3 True True 1 True True GTK_RELIEF_NORMAL True Tr