%coot-listener-socket: remote-control*annotations*: coot-utils*continue-multi-refine*: fitting*default-ball-and-stick-selection*: coot-utils*do-coot-tips-flag*: coot*imol-jligand-link*: jligand*interactive-probe-is-OK?*: generic-objects*jligand-home-env*: jligand*key-bindings*: coot-utils*pisa-command*: parse-pisa-xml*probe-command*: coot*reduce-command*: coot*to-jligand-secret-file-name*: jligand3-letter-code->single-letter: mutate-in-schemea-rapper-gui: a-rapper-guiabsolutify: coot-utilsaccept-baton-position: accept-baton-positionaccept-regularizement: accept-regularizementactive-residue: active-residueadd-action-view: add-action-viewadd-annotation-here: coot-utilsadd-coordinates-glob-extension: add-coordinates-glob-extensionadd-data-glob-extension: add-data-glob-extensionadd-dictionary-glob-extension: add-dictionary-glob-extensionadd-extra-bond-restraint: add-extra-bond-restraintadd-extra-restraints-to-other-molecule: fittingadd-key-binding: coot-utilsadd-ligand-delete-residue-copy-molecule: add-ligand-delete-residue-copy-moleculeadd-ligand-search-ligand-molecule: add-ligand-search-ligand-moleculeadd-ligand-search-wiggly-ligand-molecule: add-ligand-search-wiggly-ligand-moleculeadd-map-glob-extension: add-map-glob-extensionadd-molecule: add-moleculeadd-ncs-matrix: add-ncs-matrixadd-omega-torsion-restriants: add-omega-torsion-restriantsadd-planar-peptide-restraints: add-planar-peptide-restraintsadd-simple-coot-menu-menuitem: coot-guiadd-status-bar-text: add-status-bar-textadd-strict-ncs-matrix: add-strict-ncs-matrixadd-terminal-residue: add-terminal-residueadd-terminal-residue-do-post-refine-state: add-terminal-residue-do-post-refine-stateadd-terminal-residue-using-phi-psi: add-terminal-residue-using-phi-psiadd-tmp-extension-to: coot-utilsadd-to-list-section-texis: snarf-coot-docsadd-view: coot-utilsadd-view-description: add-view-descriptionadd-view-here: add-view-hereadd-view-raw: add-view-rawadd-view-to-views-panel: coot-guiadditional-representation-by-attributes: additional-representation-by-attributesadditional-representation-by-string: additional-representation-by-stringalign-and-mutate: align-and-mutatealign-to-closest-chain: align-to-closest-chainalignment-mismatches-gui: coot-guiall-residues: coot-utilsanother-level: another-levelanother-level-from-map-molecule-number: another-level-from-map-molecule-numberappend-dir-dir: coot-utilsappend-dir-file: coot-utilsapply-ncs-to-view-orientation: apply-ncs-to-view-orientationapply-ncs-to-view-orientation-and-screen-centre: apply-ncs-to-view-orientation-and-screen-centreassign-fasta-sequence: assign-fasta-sequenceassign-hetatms: assign-hetatmsassign-pir-sequence: assign-pir-sequenceassign-sequence-from-file: assign-sequence-from-fileassign-sequence-from-string: assign-sequence-from-stringassociate-pir-file: coot-utilsassociate-pir-with-molecule-gui: coot-guiatom-spec-to-atom-index: atom-spec-to-atom-indexatom-specs: coot-utilsauto-fit-best-rotamer: auto-fit-best-rotamerauto-fit-rotamer-active-residue: fittingauto-read-do-difference-map-too-state: auto-read-do-difference-map-too-stateauto-read-make-and-draw-maps: auto-read-make-and-draw-mapsauto-weight-for-refinement: coot-utilsbackground-demo: background-demobackground-is-black-p: background-is-black-pbackup-compress-files-state: backup-compress-files-statebackup-state: backup-stateBALL_AND_STICK: coot-utilsbaton-build-delete-last-residue: baton-build-delete-last-residuebaton-try-another: baton-try-anotherblob-under-pointer-to-screen-centre: blob-under-pointer-to-screen-centrebrief-atom-labels-state: brief-atom-labels-statebrighten-map: coot-utilsbrighten-maps: coot-utilsbrowser-url: browser-urlcache-or-net-get-image: get-recent-pdbecached-pisa-analysis: parse-pisa-xmlcalc-phases-generic: calc-phases-genericcenter-atom-label-status: americanismscenter-of-mass: americanismscentre-of-mass: coot-utilschain-ids: coot-utilschain-n-residues: chain-n-residueschange-contour-level: change-contour-levelchange-model-molecule-representation-mode: change-model-molecule-representation-modechange-residue-number: change-residue-numbercheck-chiral-volumes: check-chiral-volumescheck-dir-and-get-url: get-ebichiral-center-inverter: coot-utilschiral-centre-inverter: coot-utilscis-peptides-gui: coot-guiclear-all-fixed-atoms: clear-all-fixed-atomsclear-all-views: clear-all-viewsclear-and-update-model-molecule-from-file: clear-and-update-model-molecule-from-fileclear-and-update-molecule: clear-and-update-moleculeclear-backup-gui: clear-backupclear-backups-maybe: clear-backupclear-ball-and-stick: clear-ball-and-stickclear-dots: clear-dotsclear-dots-by-name: clear-dots-by-nameclear-pending-picks: clear-pending-picksclick-select-residues-for-jligand: jligandclose-float?: coot-utilsclose-generic-object: close-generic-objectclosest-atom: closest-atomcns->coot: cns2cootcommand-in-path-or-absolute?: coot-utilscommand-in-path?: coot-crash-catchercommand-in-path?: snarf-coot-docscommand-in-path?: coot-utilscontrol-key-for-rotate-state: control-key-for-rotate-statecoot-gui: coot-guicoot-has-pygtk?: coot-utilscoot-listener-idle-function-proc: remote-controlcoot-menubar-menu: coot-guicoot-mkdir: coot-utilscoot-real-exit: coot-real-exitcoot-socket-timeout-func: remote-controlcoot-split-version-string: coot-utilscoot-thread-dispatcher: get-recent-pdbecoot-updates-error-handler: coot-utilscoot-version: coot-versioncootaneer-gui: coot-guicopy-chain: copy-chaincopy-from-ncs-master-to-others: copy-from-ncs-master-to-otherscopy-molecule: copy-moleculecopy-residue-range: copy-residue-rangecopy-residue-range-from-ncs-master-to-others: copy-residue-range-from-ncs-master-to-otherscreate-pointer-atom-molecule-maybe: create-pointer-atom-molecule-maybedarken-maps: coot-utilsdata-resolution: data-resolutiondb-mainchain: db-mainchaindecrease-coot-tip-number: tips-guidefault-new-atoms-b-factor: default-new-atoms-b-factordelete-all-extra-restraints: delete-all-extra-restraintsdelete-all-sequences-from-molecule: delete-all-sequences-from-moleculedelete-atom: delete-atomdelete-atom-by-active-residue: coot-utilsdelete-checked-waters-baddies: delete-checked-waters-baddiesdelete-coot-backup-files: clear-backupdelete-hydrogens: delete-hydrogensdelete-residue: delete-residuedelete-residue-hydrogens: delete-residue-hydrogensdelete-residue-range: delete-residue-rangedelete-residue-sidechain: delete-residue-sidechaindelete-residue-with-full-spec: delete-residue-with-full-specdelete-section-texi-files: snarf-coot-docsdelete-sequence-by-chain-id: delete-sequence-by-chain-iddelete-sidechain-range: mutate-in-schemedensity-at-point: density-at-pointdialog-box-of-buttons: coot-guidialog-box-of-buttons-with-async-ligands: get-recent-pdbedialog-box-of-buttons-with-check-button: coot-guidialog-box-of-pairs-of-buttons: coot-guidictionaries-read: dictionaries-readdifference-map: difference-mapdifference-map-peaks: difference-map-peaksdirectory-as-file-name: coot-utilsdirectory-files: coot-crash-catcherdirectory-files: snarf-coot-docsdirectory-files: coot-utilsdirectory-is-modifiable?: coot-utilsdirectory-is-modifiable?: check-for-updatesdisplay-lists-for-maps-state: display-lists-for-maps-statedisrupt: exercise-scm-moldo-180-degree-side-chain-flip: do-180-degree-side-chain-flipdo-anti-aliasing-state: do-anti-aliasing-statedo-find-ligands-dialog: do-find-ligands-dialogdo-GL-lighting-state: do-GL-lighting-statedo-probe-dots-on-rotamers-and-chis-state: do-probe-dots-on-rotamers-and-chis-statedo-probe-dots-post-refine-state: do-probe-dots-post-refine-statedo-ramachandran-plot: do-ramachandran-plotdo-sequence-view: do-sequence-viewdo-smiles-gui: do-smiles-guido-surface: do-surfacedoes-residue-exist-p: does-residue-exist-pdots: dotsdownload-binary-dialog: check-for-updatesdrag-intermediate-atom: coot-utilsdragged-refinement-steps-per-frame: dragged-refinement-steps-per-framedraw-hydrogens-state: draw-hydrogens-statedraw-ncs-ghosts-state: draw-ncs-ghosts-stateedit-chi-angles: edit-chi-anglesesoteric-depth-cue-state: esoteric-depth-cue-stateeval-socket-string: remote-controlevery-nth: coot-utilsexchange-chain-ids-for-seg-ids: exchange-chain-ids-for-seg-idsexecute-find-blobs: execute-find-blobsexecute-find-waters-real: execute-find-waters-realexecute-refmac-real: execute-refmac-realexport-map: export-mapexport-map-fragment: export-map-fragmentextra-params-include-weight?: refmacfascinating-clusters-gui: fascinating-thingsfffear-angular-resolution: fffear-angular-resolutionfffear-search: fffear-searchfile-name-directory: coot-utilsfile-name-extension: coot-utilsfile-name-sans-extension: coot-utilsfile-selector-entry: coot-guifile-type-coords: file-type-coordsfill-option-menu-with-coordinates-mol-options: coot-guifill-option-menu-with-mol-options: coot-guifill-option-menu-with-number-options: coot-guifill-partial-residues: fill-partial-residuesfilter: coot-crash-catcherfilter: filterfilter-fileselection-filenames-state: filter-fileselection-filenames-statefind-aligned-residue-type: coot-utilsfind-helices: find-helicesfind-secondary-structure: find-secondary-structurefind-secondary-structure-local: find-secondary-structure-localfind-strands: find-strandsfirst-coords-imol: first-coords-imolfirst-molecule-with-symmetry-displayed: first-molecule-with-symmetry-displayedfirst-n: coot-utilsfirst-non-trivial-name: hellofirst-small-coords-imol: first-small-coords-imolfirst-unsaved-coords-imol: first-unsaved-coords-imolfit-chain: fittingfit-protein: fittingfit-protein-make-specs: fittingfit-residue-range-to-map-by-simplex: fit-residue-range-to-map-by-simplexfit-to-map-by-random-jiggle: fit-to-map-by-random-jigglefit-waters: fittingfix-nomenclature-errors: fix-nomenclature-errorsflip-active-ligand: coot-utilsflip-ligand: flip-ligandfull-atom-spec-to-atom-index: full-atom-spec-to-atom-indexgeneric-buttons-dialog: coot-guigeneric-chooser-and-entry: coot-guigeneric-chooser-and-file-selector: coot-guigeneric-chooser-entry-and-file-selector: coot-guigeneric-double-entry: coot-guigeneric-interesting-things: coot-guigeneric-molecule-chooser: coot-guigeneric-multiple-entries-with-check-button: coot-guigeneric-number-chooser: coot-guigeneric-object-clear: generic-object-cleargeneric-object-has-objects-p: generic-object-has-objects-pgeneric-object-index: generic-object-indexgeneric-object-info: generic-object-infogeneric-object-is-displayed-p: generic-object-is-displayed-pgeneric-object-is-displayed?: generic-objectsgeneric-object-with-name: generic-objectsgeneric-objects-gui: generic-objectsgeneric-objects-gui-wrapper: generic-objects-gui-wrappergeneric-single-entry: coot-guiget-active-map-drag-flag: get-active-map-drag-flagget-atom: coot-utilsget-atom-colour-from-mol-no: get-atom-colour-from-mol-noget-coords-for-accession-code: get-coords-for-accession-codeget-default-bond-thickness: get-default-bond-thicknessget-ebi-pdb: get-ebiget-electrostatic-surface-opacity: get-electrostatic-surface-opacityget-file-mtime: jligandget-first-ncs-master-chain: coot-utilsget-flip-residue: what-checkget-font-size: get-font-sizeget-gdb-strings: coot-crash-catcherget-map-radius: get-map-radiusget-map-sampling-rate: get-map-sampling-rateget-mdl-latest-time: prodrg-importget-molecule-bonds-colour-map-rotation: get-molecule-bonds-colour-map-rotationget-monomer: get-monomerget-option-menu-active-item: coot-guiget-option-menu-active-molecule: coot-guiget-refmac-extra-params: refmacget-reset-b-factor-moved-atoms-state: get-reset-b-factor-moved-atoms-stateget-revision-from-string: coot-utilsget-sbase-monomer: get-sbase-monomerget-show-symmetry: get-show-symmetryget-show-unit-cell: get-show-unit-cellget-smooth-scroll: get-smooth-scrollget-stable-release-from-coot-version: check-for-updatesget-stable-release-from-server-string: check-for-updatesget-symmetry: get-symmetryget-symmetry-as-calphas-state: get-symmetry-as-calphas-stateget-url-str: get-ebiget-view-quaternion-internal: get-view-quaternion-internalget-write-conect-record-state: get-write-conect-record-stategln-asn-b-factor-outliers: gln-asn-b-factor-outliersglob: coot-crash-catcherglob: snarf-coot-docsglob: coot-utilsgo-to-ligand: go-to-ligandgo-to-residue-by-spec: what-checkgoosh-command: snarf-coot-docsgoosh-command: coot-utilsgoosh-command-with-file-input: coot-utilsgraphics-comma-key-pressed-hook: coot-utilsgraphics-dot-key-pressed-hook: coot-utilsgraphics-draw: graphics-drawgraphics-general-key-press-hook: coot-utilsgraphics-molecule-bond-type: graphics-molecule-bond-typegraphics-n-molecules: graphics-n-moleculesgraphics-to-b-factor-cas-representation: graphics-to-b-factor-cas-representationgraphics-to-b-factor-representation: graphics-to-b-factor-representationgraphics-to-bonds-no-waters-representation: graphics-to-bonds-no-waters-representationgraphics-to-bonds-representation: graphics-to-bonds-representationgraphics-to-ca-plus-ligands-representation: graphics-to-ca-plus-ligands-representationgraphics-to-ca-plus-ligands-sec-struct-representation: graphics-to-ca-plus-ligands-sec-struct-representationgraphics-to-ca-representation: graphics-to-ca-representationgraphics-to-occupancy-representation: graphics-to-occupancy-representationgraphics-to-rainbow-representation: graphics-to-rainbow-representationgraphics-to-sec-struct-bonds-representation: graphics-to-sec-struct-bonds-representationguess-refinement-map: coot-utilshandle-cns-data-file: handle-cns-data-filehandle-cns-data-file-with-cell: handle-cns-data-file-with-cellhandle-drag-and-drop-string: handle-drag-and-drop-stringhandle-online-coot-search-request: handle-online-coot-search-requesthandle-read-ccp4-map: handle-read-ccp4-maphandle-read-draw-molecule: handle-read-draw-moleculehandle-read-draw-molecule-and-move-molecule-here: handle-read-draw-molecule-and-move-molecule-herehandle-read-draw-molecule-with-recenter: americanismshandle-read-draw-molecule-with-recentre: handle-read-draw-molecule-with-recentrehandle-read-draw-probe-dots: handle-read-draw-probe-dotshandle-read-draw-probe-dots-unformatted: handle-read-draw-probe-dots-unformattedhandle-smiles-go: coot-guihardware-stereo-angle-factor-state: hardware-stereo-angle-factor-statehardware-stereo-mode: hardware-stereo-modehas-unit-cell-state: has-unit-cell-statehave-unsaved-changes-p: have-unsaved-changes-phetify-residue: hetify-residuehide-main-toolbar: hide-main-toolbarhide-modelling-toolbar: hide-modelling-toolbarhilight-binding-site: coot-utilshole: holeideal-nucleic-acid: ideal-nucleic-acididentity-matrix: coot-utilsimol-refinement-map: imol-refinement-mapimport-from-3d-generator-from-mdl: prodrg-importincrement-coot-tip-number: tips-guiinfo-dialog: info-dialoginsert-action-view-after-view: insert-action-view-after-viewinsertion-code-from-serial-number: insertion-code-from-serial-numberinteractive-probe: generic-objectsinteractive-probe-dots-molprobity-radius: interactive-probe-dots-molprobity-radiusinteresting-things-gui: coot-guiinteresting-things-with-fix-maybe: coot-guiinterruptible-fit-protein: fittingis-closed-generic-object-p: is-closed-generic-object-pis-closed-generic-object?: generic-objectsis-difference-map?: coot-utilsis-directory?: coot-utilsis-solvent-chain-p: is-solvent-chain-pis-solvent-chain?: coot-utilsjiggled-mol: exercise-scm-molkeep-map-colour-after-refmac-state: keep-map-colour-after-refmac-statelabel-all-active-residue-atoms: coot-utilslabel-all-atoms-in-residue: coot-utilslabel-all-CAs: coot-utilslaplacian: laplacianlaunch-jligand-function: jligandlengthen-baton: lengthen-batonlibcheck-exe: libcheckligand-expert: ligand-expertlist-of-strings?: coot-utilsload-all-scheme: cootload-annotations: coot-utilsload-default-sequence: coot-utilslsq-improve: lsq-improvelsq-match: coot-lsqlsq-match-type-symbol->number: coot-lsqlsqman-count: brute-lsqmanmaf: mutate-in-schememake-and-draw-map: make-and-draw-mapmake-and-draw-map-with-refmac-params: make-and-draw-map-with-refmac-paramsmake-and-draw-map-with-reso-with-refmac-params: make-and-draw-map-with-reso-with-refmac-paramsmake-and-draw-patterson: make-and-draw-pattersonmake-backup: make-backupmake-ball-and-stick: make-ball-and-stickmake-difference-map-gui: coot-guimake-directory-maybe: make-directory-maybemake-dynamically-transformed-ncs-maps: make-dynamically-transformed-ncs-mapsmake-gdb-script: coot-crash-catchermake-gui: coot-crash-catchermake-latest-version-url: coot-utilsmake-socket-listener-maybe: make-socket-listener-maybemanage-column-selector: manage-column-selectormanual-ncs-ghosts: ncsmanual-refine-residues: fittingmap-colour-components: map-colour-componentsmap-from-mtz-by-calc-phases: map-from-mtz-by-calc-phasesmap-from-mtz-by-refmac-calc-phases: map-from-mtz-by-refmac-calc-phasesmap-is-displayed: map-is-displayedmap-line-width-state: map-line-width-statemap-mask-atom-radius: map-mask-atom-radiusmap-molecule-chooser-gui: coot-guimap-molecule-list: coot-utilsmask-map-by-molecule: mask-map-by-moleculematch-ligand-atom-names: match-ligand-atom-namesmatrix->quaternion: coot-utilsmatrix->quaternion: quat-convertmatrix-state: matrix-statemax-water-distance: max-water-distancemember?: coot-utilsmerge-solvent-chains: coot-utilsmin-max-residues-from-atom-specs: coot-guimissing-atoms-gui: coot-guimmcif-sfs-to-mtz: mmcif-sfs-to-mtzmodel-molecule-list: coot-utilsmodel-resolution: model-resolutionmol-is-active: mol-is-activemol-is-displayed: mol-is-displayedmolecule-centre: coot-utilsmolecule-centres-gui: coot-guimolecule-chooser-gui: coot-guimolecule-chooser-gui-generic: coot-guimolecule-has-hydrogens?: coot-utilsmolecule-name: molecule-namemolecule-number-list: coot-utilsmolecules-matching-criteria: fittingmono-mode: mono-modemonomer-molecule-from-3-let-code: libcheckmost-recently-created-file: coot-utilsmove-hetgroups-to-around-protein: move-hetgroups-to-around-proteinmove-molecule-here: coot-utilsmove-molecule-to-screen-center: coot-utilsmove-molecule-to-screen-centre: coot-utilsmove-waters-to-around-protein: move-waters-to-around-proteinmtz-fp-for-map: mtz-fp-for-mapmtz-hklin-for-map: mtz-hklin-for-mapmtz-phi-for-map: mtz-phi-for-mapmtz-use-weight-for-map: mtz-use-weight-for-mapmtz-weight-for-map: mtz-weight-for-mapmulti-chicken: coot-utilsmulti-mutate: mutate-in-schememulti-read-pdb: coot-utilsmulti-residue-torsion-fit-scm: multi-residue-torsion-fit-scmmutate: mutatemutate-and-auto-fit: mutate-in-schememutate-and-autofit-residue-range: mutate-in-schememutate-auto-fit-do-post-refine-state: mutate-auto-fit-do-post-refine-statemutate-base: mutate-basemutate-by-overlap: coot-utilsmutate-chain: mutate-in-schememutate-residue-range: mutate-in-schememutate-residue-redundant: mutate-in-schememutate-single-residue-by-serial-number: mutate-single-residue-by-serial-numbermy-button-callback: extra-top-levelmy-top-level: extra-top-leveln-chains: n-chainsn-dots-sets: n-dots-setsn-models: n-modelsn-residues: n-residuesn-rotamers: n-rotamersncs-control-change-ncs-master-to-chain: ncs-control-change-ncs-master-to-chainncs-control-change-ncs-master-to-chain-id: ncs-control-change-ncs-master-to-chain-idncs-control-display-chain: ncs-control-display-chainncs-ligand: ncsncs-master-chain-id: ncsncs-update-ghosts: ncs-update-ghostsnew-generic-object-number: new-generic-object-numbernew-molecule-by-atom-selection: new-molecule-by-atom-selectionnew-molecule-by-residue-type-selection: new-molecule-by-residue-type-selectionnew-molecule-by-smiles-string: coot-utilsnew-molecule-by-sphere-selection: new-molecule-by-sphere-selectionnew-molecule-by-symmetry: new-molecule-by-symmetrynew-molecule-by-symmetry-with-atom-selection: new-molecule-by-symmetry-with-atom-selectionnew-molecule-by-symop: new-molecule-by-symopno-coot-tips: tipsnotify-of-new-version: check-for-updatesnudge-screen-centre-gui: coot-guinumber-list: coot-utilsnumber-of-generic-objects: number-of-generic-objectsold-coot?: coot-guiopen-cif-dictionary-file-selector-dialog: open-cif-dictionary-file-selector-dialogopen-coords-dialog: open-coords-dialogopen-coot-listener-socket: remote-controlopen-coot-listener-socket-with-timeout: remote-controloutput-atom-info-as-text: output-atom-info-as-textoverlay-my-ligands: coot-utilsparse-check-db: what-checkparse-pisa-assemblies: parse-pisa-xmlparse-pisa-interfaces: parse-pisa-xmlpdbe-get-pdb-and-sfs-cif: get-recent-pdbepdbe-latest-releases-gui: get-recent-pdbepepflip: pepflippepflip-active-residue: fittingphosphorylate-active-residue: coot-utilspir-file-name->pir-sequence: coot-utilspisa-assemblies-xml: parse-pisa-xmlpisa-handle-sxml-molecule: parse-pisa-xmlpisa-interaction: pisa-interactionplace-helix-here: place-helix-hereplace-strand-here: place-strand-hereplace-strand-here-dialog: place-strand-here-dialogplace-text: place-textpointer-atom-molecule: pointer-atom-moleculepost-display-control-window: post-display-control-windowpost-go-to-atom-window: post-go-to-atom-windowpost-ligand-fit-gui: fittingpost-manipulation-hook: coot-utilspost-model-fit-refine-dialog: post-model-fit-refine-dialogpost-other-modelling-tools-dialog: post-other-modelling-tools-dialogpost-python-scripting-window: post-python-scripting-windowpost-scheme-scripting-window: post-scheme-scripting-windowpost-scripting-window: post-scripting-windowpovray-args: mutate-from-schemepovray-image: mutate-from-schemepovray-version: mutate-from-schemepre-release?: coot-utilsprefer-python: prefer-pythonprep-for-pisa: parse-pisa-xmlprint-all-history-in-python: print-all-history-in-pythonprint-all-history-in-scheme: print-all-history-in-schemeprint-header-secondary-structure-info: print-header-secondary-structure-infoprint-molecule-names: coot-utilsprint-sequence: coot-utilsprint-sequence-chain: print-sequence-chainprint-view-matrix: print-view-matrixprobe: generic-objectsprobe-available-p: probe-available-pprobe-local-sphere: generic-objectsproblem-residues->dialog: what-checkprodrg-flat: prodrg-importprodrg-ify: coot-utilsprodrg-xyzin: prodrg-importprotein-db-loops: protein-db-loopspukka-puckers?: coot-utilsquick-save: quick-saveramachandran-plot-differences: ramachandran-plot-differencesramachandran-plot-differences-by-chain: ramachandran-plot-differences-by-chainrange: coot-utilsrapper-dir: a-rapper-guirapper-dir: group-settingsraster-screen-shot: raster-screen-shotraster3d: raster3draytrace: raster3d-from-schemeread-pdb: read-pdbread-pdb-all: coot-utilsread-phs-and-coords-and-make-map: read-phs-and-coords-and-make-mapread-phs-and-make-map-using-cell-symm: read-phs-and-make-map-using-cell-symmread-phs-and-make-map-using-cell-symm-from-mol: read-phs-and-make-map-using-cell-symm-from-molread-phs-and-make-map-using-cell-symm-from-previous-mol: read-phs-and-make-map-using-cell-symm-from-previous-molread-phs-and-make-map-with-reso-limits: read-phs-and-make-map-with-reso-limitsread-shelx-ins-file: read-shelx-ins-fileread-shelx-lst-file: shelxread-vu-file: coot-utilsreattach-modelling-toolbar: reattach-modelling-toolbarrecover-session: recover-sessionredraw-background: redraw-backgroundreduce-on-pdb-file: generic-objectsrefine-active-residue: fittingrefine-active-residue-generic: fittingrefine-active-residue-triple: fittingrefine-auto-range: refine-auto-rangerefine-with-torsion-restraints-state: refine-with-torsion-restraints-staterefine-zone: refine-zonerefine-zone-atom-index-define: refine-zone-atom-index-definerefine-zone-with-full-residue-spec-scm: refine-zone-with-full-residue-spec-scmrefinement-immediate-replacement-state: refinement-immediate-replacement-staterefinement-move-atoms-with-zero-occupancy-state: refinement-move-atoms-with-zero-occupancy-staterefinement-refine-per-frame-state: refinement-refine-per-frame-staterefmac-calc-sfs-make-mtz: get-recent-pdberefmac-exe: refmacrefmac-extra-params: refmacrefmac-name: refmac-namerefmac-problems-gui: refmac-problemsregularize-zone: regularize-zoneremarks-dialog: remarks-dialogremove-coordinates-glob-extension: remove-coordinates-glob-extensionremove-data-glob-extension: remove-data-glob-extensionremove-dictionary-glob-extension: remove-dictionary-glob-extensionremove-map-glob-extension: remove-map-glob-extensionremove-named-view: remove-named-viewremove-omega-torsion-restriants: remove-omega-torsion-restriantsremove-planar-peptide-restraints: remove-planar-peptide-restraintsremove-text: remove-textremove-view: remove-viewrename-residue-gui: coot-guirender-image: raster3d-from-schemerenumber-residue-range: renumber-residue-rangereorder-chains: coot-utilsreplace-fragment: replace-fragmentres-spec->chain-id: coot-utilsres-spec->ins-code: coot-utilsres-spec->res-no: coot-utilsreset-view: reset-viewresidue-alt-confs: coot-utilsresidue-density-fit-scale-factor: residue-density-fit-scale-factorresidue-exists?: coot-utilsresidue-has-hetatms: residue-has-hetatmsresidue-has-hetatms?: coot-utilsresidue-info: residue-inforesidue-range-gui: coot-guiresidue-spec->atom-for-centre: coot-utilsresidue-spec->atom-selection-string: coot-utilsresidue-spec->string: what-checkresidues-matching-criteria: coot-utilsresidues-near-residue: residues-near-residueresidues-with-alt-confs: coot-utilsresname-from-serial-number: resname-from-serial-numberrestore-previous-map-colour: restore-previous-map-colourrigid-body-refine-by-residue-ranges: coot-utilsrigid-body-refine-zone: rigid-body-refine-zonerotamer-auto-fit-do-post-refine-state: rotamer-auto-fit-do-post-refine-staterotate-about-screen-axis: coot-utilsrotate-x-scene: rotate-x-scenerotate-y-scene: rotate-y-scenerotate-z-scene: rotate-z-scenerotation-centre: coot-utilsrun-command/strings: coot-crash-catcherrun-command/strings: snarf-coot-docsrun-command/strings: coot-utilsrun-download-binary-curl: coot-utilsrun-gtk-pending-events: coot-guirun-refmac-by-filename: refmacrun-refmac-for-phases: refmacrun-script: run-scriptrun-state-file: run-state-filerun-state-file-maybe: run-state-file-maybesanitise-alt-confs: coot-utilssanitise-alt-confs-active-residue: coot-utilssanitise-alt-confs-in-residue: coot-utilssave-annotations: coot-utilssave-coordinates: save-coordinatessave-dialog-positions-to-init-file: coot-utilssave-previous-map-colour: save-previous-map-coloursave-state: save-statesave-state-file: save-state-filesave-symmetry-coords: save-symmetry-coordssave-views: save-viewsscale-cell: scale-cellscale-zoom: scale-zoomscheme-representation: coot-utilsscore-residue-range-fit-to-map: score-residue-range-fit-to-mapscreendump-image: screendump-imagescroll-by-wheel-mouse-state: scroll-by-wheel-mouse-statescroll-wheel-map: scroll-wheel-mapsecondary-structure-restraints-type: secondary-structure-restraints-typeseqnum-from-serial-number: seqnum-from-serial-numberset-accept-reject-dialog-position: set-accept-reject-dialog-positionset-active-map-drag-flag: set-active-map-drag-flagset-add-terminal-residue-default-residue-type: set-add-terminal-residue-default-residue-typeset-add-terminal-residue-do-post-refine: set-add-terminal-residue-do-post-refineset-add-terminal-residue-immediate-addition: set-add-terminal-residue-immediate-additionset-alignment-gap-and-space-penalty: set-alignment-gap-and-space-penaltyset-all-maps-displayed: set-all-maps-displayedset-all-models-displayed-and-active: set-all-models-displayed-and-activeset-atom-attribute: set-atom-attributeset-atom-string-attribute: set-atom-string-attributeset-auto-fit-best-rotamer-clash-flag: set-auto-fit-best-rotamer-clash-flagset-auto-read-column-labels: set-auto-read-column-labelsset-auto-read-do-difference-map-too: set-auto-read-do-difference-map-tooset-b-factor-bonds-scale-factor: set-b-factor-bonds-scale-factorset-background-colour: set-background-colourset-backup-compress-files: set-backup-compress-filesset-baton-build-params: set-baton-build-paramsset-baton-mode: set-baton-modeset-bond-thickness: set-bond-thicknessset-bond-thickness-intermediate-atoms: set-bond-thickness-intermediate-atomsset-brief-atom-labels: set-brief-atom-labelsset-browser-interface: set-browser-interfaceset-button-label-for-external-refinement: set-button-label-for-external-refinementset-colour-by-chain: set-colour-by-chainset-colour-by-molecule: set-colour-by-moleculeset-colour-map-rotation-for-map: set-colour-map-rotation-for-mapset-colour-map-rotation-on-read-pdb: set-colour-map-rotation-on-read-pdbset-colour-map-rotation-on-read-pdb-c-only-flag: set-colour-map-rotation-on-read-pdb-c-only-flagset-colour-map-rotation-on-read-pdb-flag: set-colour-map-rotation-on-read-pdb-flagset-console-display-commands-hilights: set-console-display-commands-hilightsset-console-display-commands-state: set-console-display-commands-stateset-contour-by-sigma-step-by-mol: set-contour-by-sigma-step-by-molset-control-key-for-rotate: set-control-key-for-rotateset-convert-to-v2-atom-names: set-convert-to-v2-atom-namesset-default-bond-thickness: set-default-bond-thicknessset-default-initial-contour-level-for-difference-map: set-default-initial-contour-level-for-difference-mapset-default-initial-contour-level-for-map: set-default-initial-contour-level-for-mapset-default-representation-type: set-default-representation-typeset-default-temperature-factor-for-new-atoms: set-default-temperature-factor-for-new-atomsset-delete-dialog-position: set-delete-dialog-positionset-density-size: set-density-sizeset-diff-map-iso-level-increment: set-diff-map-iso-level-incrementset-display-control-dialog-position: set-display-control-dialog-positionset-display-generic-object: set-display-generic-objectset-display-intro-string: set-display-intro-stringset-display-lists-for-maps: set-display-lists-for-mapsset-do-anti-aliasing: set-do-anti-aliasingset-do-GL-lighting: set-do-GL-lightingset-do-probe-dots-on-rotamers-and-chis: set-do-probe-dots-on-rotamers-and-chisset-do-probe-dots-post-refine: set-do-probe-dots-post-refineset-dots-color: americanismsset-dots-colour: set-dots-colourset-dragged-refinement-steps-per-frame: set-dragged-refinement-steps-per-frameset-draw-crosshairs: set-draw-crosshairsset-draw-hydrogens: set-draw-hydrogensset-draw-map-standard-lines: set-draw-map-standard-linesset-draw-ncs-ghosts: set-draw-ncs-ghostsset-draw-solid-density-surface: set-draw-solid-density-surfaceset-draw-zero-occ-markers: set-draw-zero-occ-markersset-edit-chi-angles-dialog-position: set-edit-chi-angles-dialog-positionset-environment-distances-distance-limits: set-environment-distances-distance-limitsset-esoteric-depth-cue: set-esoteric-depth-cueset-fffear-angular-resolution: set-fffear-angular-resolutionset-filter-fileselection-filenames: set-filter-fileselection-filenamesset-find-hydrogen-torsion: coot-utilsset-find-hydrogen-torsions: set-find-hydrogen-torsionsset-find-ligand-mask-waters: set-find-ligand-mask-watersset-find-ligand-n-top-ligands: set-find-ligand-n-top-ligandsset-fix-chiral-volumes-before-refinement: set-fix-chiral-volumes-before-refinementset-flat-shading-for-solid-density-surface: set-flat-shading-for-solid-density-surfaceset-font-color: americanismsset-font-colour: set-font-colourset-font-size: set-font-sizeset-go-to-atom-chain-residue-atom-name: set-go-to-atom-chain-residue-atom-nameset-go-to-atom-molecule: set-go-to-atom-moleculeset-go-to-atom-window-position: set-go-to-atom-window-positionset-graphics-window-position: set-graphics-window-positionset-graphics-window-size: set-graphics-window-sizeset-hardware-stereo-angle-factor: set-hardware-stereo-angle-factorset-have-unsaved-changes: set-have-unsaved-changesset-idle-function-rotate-angle: set-idle-function-rotate-angleset-imol-refinement-map: set-imol-refinement-mapset-interactive-probe-dots-molprobity-radius: set-interactive-probe-dots-molprobity-radiusset-iso-level-increment: set-iso-level-incrementset-keep-map-colour-after-refmac: set-keep-map-colour-after-refmacset-kleywegt-plot-n-diffs: set-kleywegt-plot-n-diffsset-last-map-color: americanismsset-last-map-colour: set-last-map-colourset-last-map-contour-level: set-last-map-contour-levelset-last-map-contour-level-by-sigma: set-last-map-contour-level-by-sigmaset-last-map-sigma-step: set-last-map-sigma-stepset-ligand-acceptable-fit-fraction: set-ligand-acceptable-fit-fractionset-ligand-cluster-sigma-level: set-ligand-cluster-sigma-levelset-ligand-flexible-ligand-n-samples: set-ligand-flexible-ligand-n-samplesset-ligand-search-map-molecule: set-ligand-search-map-moleculeset-ligand-search-protein-molecule: set-ligand-search-protein-moleculeset-ligand-water-n-cycles: set-ligand-water-n-cyclesset-ligand-water-to-protein-distance-limits: set-ligand-water-to-protein-distance-limitsset-map-colour: set-map-colourset-map-displayed: set-map-displayedset-map-is-difference-map: set-map-is-difference-mapset-map-line-width: set-map-line-widthset-map-mask-atom-radius: set-map-mask-atom-radiusset-map-radius: set-map-radiusset-map-sampling-rate: set-map-sampling-rateset-map-sharpening-scale-limit: set-map-sharpening-scale-limitset-match-element: coot-lsqset-matrix: set-matrixset-max-skeleton-search-depth: set-max-skeleton-search-depthset-model-fit-refine-dialog-position: set-model-fit-refine-dialog-positionset-model-fit-refine-place-atom-at-pointer-label: set-model-fit-refine-place-atom-at-pointer-labelset-model-fit-refine-rotate-translate-zone-label: set-model-fit-refine-rotate-translate-zone-labelset-model-toolbar-docked-position: set-model-toolbar-docked-positionset-mol-active: set-mol-activeset-mol-displayed: set-mol-displayedset-molecule-bonds-colour-map-rotation: set-molecule-bonds-colour-map-rotationset-molecule-name: set-molecule-nameset-monomer-restraints: set-monomer-restraintsset-mutate-auto-fit-do-post-refine: set-mutate-auto-fit-do-post-refineset-ncs-ghost-bond-thickness: set-ncs-ghost-bond-thicknessset-ncs-homology-level: set-ncs-homology-levelset-nomenclature-errors-on-read: set-nomenclature-errors-on-readset-pick-cursor-index: set-pick-cursor-indexset-prefer-python: set-prefer-pythonset-ramachandran-plot-background-block-size: set-ramachandran-plot-background-block-sizeset-ramachandran-plot-contour-levels: set-ramachandran-plot-contour-levelsset-ramachandran-plot-dialog-position: set-ramachandran-plot-dialog-positionset-raster3d-atom-radius: set-raster3d-atom-radiusset-raster3d-bond-thickness: set-raster3d-bond-thicknessset-raster3d-bone-thickness: set-raster3d-bone-thicknessset-raster3d-density-thickness: set-raster3d-density-thicknessset-raster3d-shadows-enabled: set-raster3d-shadows-enabledset-raster3d-water-sphere: set-raster3d-water-sphereset-refine-auto-range-step: set-refine-auto-range-stepset-refine-max-residues: set-refine-max-residuesset-refine-ramachandran-angles: set-refine-ramachandran-anglesset-refine-with-torsion-restraints: set-refine-with-torsion-restraintsset-refinement-immediate-replacement: set-refinement-immediate-replacementset-refinement-move-atoms-with-zero-occupancy: set-refinement-move-atoms-with-zero-occupancyset-refinement-refine-per-frame: set-refinement-refine-per-frameset-refmac-counter: set-refmac-counterset-renderer-show-atoms: set-renderer-show-atomsset-reset-b-factor-moved-atoms: set-reset-b-factor-moved-atomsset-residue-density-fit-scale-factor: set-residue-density-fit-scale-factorset-residue-name: set-residue-nameset-residue-selection-flash-frames-number: set-residue-selection-flash-frames-numberset-residue-to-rotamer-number: set-residue-to-rotamer-numberset-residue-type-chooser-stub-state: set-residue-type-chooser-stub-stateset-rigid-body-fit-acceptable-fit-fraction: set-rigid-body-fit-acceptable-fit-fractionset-rocking-factors: set-rocking-factorsset-rotamer-auto-fit-do-post-refine: set-rotamer-auto-fit-do-post-refineset-rotamer-check-clashes: set-rotamer-check-clashesset-rotamer-lowest-probability: set-rotamer-lowest-probabilityset-rotamer-search-mode: set-rotamer-search-modeset-rotamer-selection-dialog-position: set-rotamer-selection-dialog-positionset-rotate-translate-dialog-position: set-rotate-translate-dialog-positionset-rotation-center: americanismsset-rotation-center-size: americanismsset-run-state-file-status: set-run-state-file-statusset-save-state-file-name: set-save-state-file-nameset-scroll-by-wheel-mouse: set-scroll-by-wheel-mouseset-scroll-wheel-map: set-scroll-wheel-mapset-scrollable-map: set-scrollable-mapset-secondary-structure-restraints-type: set-secondary-structure-restraints-typeset-show-chiral-volume-errors-dialog: set-show-chiral-volume-errors-dialogset-show-environment-distances: set-show-environment-distancesset-show-environment-distances-bumps: set-show-environment-distances-bumpsset-show-environment-distances-h-bonds: set-show-environment-distances-h-bondsset-show-graphics-ligand-view: set-show-graphics-ligand-viewset-show-origin-marker: set-show-origin-markerset-show-paths-in-display-manager: set-show-paths-in-display-managerset-show-pointer-distances: set-show-pointer-distancesset-show-strict-ncs: set-show-strict-ncsset-show-symmetry-master: set-show-symmetry-masterset-show-symmetry-molecule: set-show-symmetry-moleculeset-show-unit-cell: set-show-unit-cellset-show-unit-cells-all: set-show-unit-cells-allset-skeleton-box-size: set-skeleton-box-sizeset-smooth-scroll-do-zoom: set-smooth-scroll-do-zoomset-smooth-scroll-flag: set-smooth-scroll-flagset-smooth-scroll-limit: set-smooth-scroll-limitset-smooth-scroll-steps: set-smooth-scroll-stepsset-solid-density-surface-opacity: set-solid-density-surface-opacityset-space-group: set-space-groupset-sticky-sort-by-date: set-sticky-sort-by-dateset-stop-scroll-diff-map: set-stop-scroll-diff-mapset-stop-scroll-diff-map-level: set-stop-scroll-diff-map-levelset-stop-scroll-iso-map: set-stop-scroll-iso-mapset-stop-scroll-iso-map-level: set-stop-scroll-iso-map-levelset-swap-difference-map-colors: americanismsset-swap-difference-map-colours: set-swap-difference-map-coloursset-symmetry-colour: set-symmetry-colourset-symmetry-molecule-rotate-colour-map: set-symmetry-molecule-rotate-colour-mapset-symmetry-shift-search-size: set-symmetry-shift-search-sizeset-symmetry-size: set-symmetry-sizeset-transparent-electrostatic-surface: set-transparent-electrostatic-surfaceset-undo-molecule: set-undo-moleculeset-unpathed-backup-file-names: set-unpathed-backup-file-namesset-view-matrix: coot-utilsset-view-matrix: quat-convertset-view-quaternion: set-view-quaternionset-virtual-trackball-type: coot-utilsset-water-check-spherical-variance-limit: set-water-check-spherical-variance-limitset-write-conect-record-state: set-write-conect-record-statesetup-mutate-auto-fit: setup-mutate-auto-fitsetup-torsion-general: setup-torsion-generalsharpen: sharpenshell-command-to-file-with-data: coot-utilsshell-command-to-string: coot-utilsshelx-molecule?: coot-utilsshelxl-refine: shelxshelxl-refine-primitive: shelxshorten-baton: shorten-batonshow-coot-tip-from-list: tips-guishow-environment-distances-state: show-environment-distances-stateshow-main-toolbar: show-main-toolbarshow-model-toolbar-all-icons: show-model-toolbar-all-iconsshow-model-toolbar-main-icons: show-model-toolbar-main-iconsshow-modelling-toolbar: show-modelling-toolbarshow-origin-marker-state: show-origin-marker-stateshow-partial-charge-info: show-partial-charge-infoshow-paths-in-display-manager-state: show-paths-in-display-manager-stateshow-pointer-distances-state: show-pointer-distances-stateshow-select-map-dialog: show-select-map-dialogshow-set-undo-molecule-chooser: show-set-undo-molecule-choosershow-spacegroup: show-spacegroupshow-strict-ncs-state: show-strict-ncs-stateside-by-side-stereo-mode: side-by-side-stereo-modesimple-lsq-match: coot-lsqsingle-manual-ncs-ghost: ncssingle-model-view-model-number: single-model-view-model-numbersingle-model-view-next-model-number: single-model-view-next-model-numbersingle-model-view-prev-model-number: single-model-view-prev-model-numbersingle-model-view-this-model-number: single-model-view-this-model-numberskeletonize-map: skeletonize-mapskip-to-next-ncs-chain: ncsslash-start?: coot-utilssmiles-gui: coot-guismooth-scroll-do-zoom: smooth-scroll-do-zoomsort-chains: sort-chainssort-residues: sort-residuesspin-search: spin-searchspin-zoom-trans: spin-zoom-transstart-graphics-interface: start-graphics-interfacestart-jligand-listener: jligandstepped-refine-protein: fittingstepped-refine-protein-for-rama: fittingstepped-refine-protein-with-refine-func: fittingstereo-mode-state: stereo-mode-statestring->list-of-strings: snarf-coot-docsstring->list-of-strings: coot-utilsstring-append-with-spaces: coot-utilsstring-append-with-string: coot-utilsstring-concatenate: coot-crash-catcherstring-concatenate: coot-utilsstring-member?: coot-utilsstrip-extension: snarf-coot-docsstrip-extension: coot-utilsstrip-leading-spaces: coot-utilsstrip-leading-spaces: what-checkstrip-path: coot-utilsstrip-spaces: coot-utilssuck-model-fit-dialog: suck-model-fit-dialogsuperpose: superposesuperpose-with-atom-selection: superpose-with-atom-selectionsuperpose-with-chain-selection: superpose-with-chain-selectionsvn-revision: svn-revisionswap-map-colours: swap-map-colourssymmetry-as-calphas: symmetry-as-calphassymmetry-molecule-rotate-colour-map-state: symmetry-molecule-rotate-colour-map-statetarget-auto-weighting-value: coot-utilsteb: entry+do-buttonteb2: entry+do-buttontext-index-near-position: text-index-near-positiontip-list: tipstips-gui: tips-guito-generic-object-add-arc: to-generic-object-add-arcto-generic-object-add-dashed-line: to-generic-object-add-dashed-lineto-generic-object-add-display-list-handle: to-generic-object-add-display-list-handleto-generic-object-add-line: to-generic-object-add-lineto-generic-object-add-point: to-generic-object-add-pointtoggle-active-mol: coot-utilstoggle-display-map: coot-utilstoggle-display-mol: coot-utilstoggle-idle-rock-function: toggle-idle-rock-functiontoggle-idle-spin-function: toggle-idle-spin-functiontransform-coords-molecule: coot-utilstransform-map: coot-utilstransform-map-using-lsq-matrix: coot-utilstransform-molecule-by: transform-molecule-bytranslate-molecule-by: translate-molecule-bytranslation: coot-utilstrim-molecule-by-map: trim-molecule-by-maptry-set-draw-baton: try-set-draw-batonturn-off-backup: turn-off-backupturn-on-backup: turn-on-backupundo-last-move: undo-last-moveundo-symmetry-view: undo-symmetry-viewunique-date/time-str: coot-utilsunmangle-hydrogen-name: unmangle-hydrogen-nameunpathed-backup-file-names-state: unpathed-backup-file-names-stateunset-sticky-sort-by-date: unset-sticky-sort-by-dateunskeletonize-map: unskeletonize-mapupdate-go-to-atom-from-current-atom: coot-utilsupdate-go-to-atom-from-current-position: update-go-to-atom-from-current-positionupdate-go-to-atom-window-on-changed-mol: update-go-to-atom-window-on-changed-molupdate-go-to-atom-window-on-new-mol: update-go-to-atom-window-on-new-molupdate-self: coot-utilsuse-graphics-interface-state: use-graphics-interface-stateuser-mods-gui: coot-guivalid-labels: valid-labelsvalid-map-molecule?: coot-utilsvalid-model-molecule?: coot-utilsvalid-refinement-map?: coot-utilsview-matrix: coot-utilsview-quaternion: coot-utilsview-saver-gui: coot-guiviews-panel-gui: coot-guivt-surface: vt-surfacevt-surface-status: vt-surface-statuswater-chain-from-shelx-ins-scm: water-chain-from-shelx-ins-scmwater-chain-scm: water-chain-scmwater-coordination-gui: coot-guiwatson-crick-pair: watson-crick-pairwatson-crick-pair-for-residue-range: watson-crick-pair-for-residue-rangewrite-ccp4mg-picture-description: write-ccp4mg-picture-descriptionwrite-pdb-file: write-pdb-filewrite-reduce-het-dict: generic-objectswrite-residue-range-to-pdb-file: write-residue-range-to-pdb-filewrite-shelx-ins-file: write-shelx-ins-filezalman-stereo-mode: zalman-stereo-modezoom-factor: zoom-factor