Pauls-key-bindings-for-coot
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(add-key-binding "Refine Active Residue" "r" (lambda () (manual-refine-residues 0)))
(add-key-binding "Refine Active Residue AA" "x" (lambda () (refine-active-residue)))
(add-key-binding "Triple Refine" "t" (lambda () (manual-refine-residues 1)))
(add-key-binding "Autofit Rotamer" "j" (lambda () (auto-fit-rotamer-active-residue)))
(add-key-binding "Pepflip" "q" (lambda () (pepflip-active-residue)))
(add-key-binding "Go To Blob" "g" (lambda () (blob-under-pointer-to-screen-centre)))
(add-key-binding "Add Water" "w" (lambda () (place-typed-atom-at-pointer "Water")))
(add-key-binding "Eigen-flip Ligand" "e" (lambda() (flip-active-ligand)))
(add-key-binding "Add terminal residue" "y" (lambda ()
(let ((active-atom (active-residue)))
(if (not active-atom)
(format #t "No active atom~%")
(let ((imol (list-ref active-atom 0))
(chain-id (list-ref active-atom 1))
(res-no (list-ref active-atom 2))
(ins-code (list-ref active-atom 3))
(atom-name (list-ref active-atom 4))
(alt-conf (list-ref active-atom 5)))
(add-terminal-residue imol chain-id res-no "auto" 1))))))
(add-key-binding "Fill Partial" "k" (lambda ()
(let ((active-atom (active-residue)))
(if (not active-atom)
(format #t "No active atom~%")
(let ((imol (list-ref active-atom 0))
(chain-id (list-ref active-atom 1))
(res-no (list-ref active-atom 2))
(ins-code (list-ref active-atom 3))
(atom-name (list-ref active-atom 4))
(alt-conf (list-ref active-atom 5)))
(fill-partial-residue imol chain-id res-no ins-code))))))
(add-key-binding "Kill Sidechain" "K"
(lambda ()
(using-active-atom
(delete-residue-sidechain aa-imol aa-chain-id aa-res-no aa-ins-code 0))))
(define *refine-residue-sphere-radius* 3.5) ;; Angstroms
(add-key-binding "Refine residues in a sphere" "R"
(lambda ()
(let ((active-atom (active-residue)))
(if (not (list? active-atom))
(format #t "No active atom~%")
(let* ((centred-residue (list-head (cdr active-atom) 3))
(imol (car active-atom))
(other-residues (residues-near-residue imol centred-residue *refine-residue-sphere-radius*))
(all-residues (if (list? other-residues)
(cons centred-residue other-residues)
(list centred-residue))))
(refine-residues imol all-residues))))))
(add-key-binding "Neighbours Refine" "h"
(lambda ()
(if (not (valid-map-molecule? (imol-refinement-map)))
(info-dialog "Must set the refinement map"))
(using-active-atom
(let* ((rc-spec (list aa-chain-id aa-res-no aa-ins-code))
(ls (residues-near-residue aa-imol rc-spec 1.9)))
(with-auto-accept
(refine-residues aa-imol (cons rc-spec ls)))))))
(add-key-binding "Load RNAs files" "F9"
(lambda ()
(let* ((home (getenv "HOME"))
(dir-1 (append-dir-dir home "data"))
(dir-2 (append-dir-dir dir-1 "rnase")))
(read-pdb (append-dir-file dir-2 "tutorial-modern.pdb"))
(make-and-draw-map (append-dir-file dir-2
"rnasa-1.8-all_refmac1.mtz")
"/RNASE3GMP/COMPLEX/FWT"
"/RNASE3GMP/COMPLEX/PHWT" "" 0 0))))
(add-key-binding "Toggle Ghosts" ":"
(lambda ()
(let ((keyboard-ghosts-mol
(let ((ls (model-molecule-list)))
(let loop ((ls ls))
(cond
((null? ls) -1)
((ncs-ghosts (car ls))
(car ls))
(else
(loop (cdr ls))))))))
(if (= (draw-ncs-ghosts-state keyboard-ghosts-mol) 0)
(set-draw-ncs-ghosts keyboard-ghosts-mol 1)
(set-draw-ncs-ghosts keyboard-ghosts-mol 0)))))
(add-key-binding "Hydrogens off" "["
(lambda ()
(let ((imol
(let ((active-atom (active-residue)))
(if active-atom
(car active-atom)
0))))
(set-draw-hydrogens imol 0))))
(add-key-binding "Hydrogens on" "]"
(lambda ()
(let ((imol
(let ((active-atom (active-residue)))
(if active-atom
(car active-atom)
0))))
(set-draw-hydrogens imol 1))))
(add-key-binding "Rotamer name in Status Bar" "~"
(lambda ()
(let ((active-atom (active-residue)))
(if (not active-residue)
(add-status-bar-text "No residue found")
(let ((imol (list-ref active-atom 0))
(chain-id (list-ref active-atom 1))
(res-no (list-ref active-atom 2))
(ins-code (list-ref active-atom 3))
(atom-name (list-ref active-atom 4))
(alt-conf (list-ref active-atom 5)))
(let ((name (get-rotamer-name imol chain-id res-no ins-code)))
(if (not name)
(add-status-bar-text "No name found")
(if (string=? "" name)
(add-status-bar-text "No name for this")
(add-status-bar-text (string-append "Rotamer name: " name))))))))))
(add-key-binding "Regularize Residues" "B"
(lambda ()
(using-active-atom
(regularize-zone aa-imol aa-chain-id (- aa-res-no 1) (+ aa-res-no 1) aa-alt-conf))))
(add-key-binding "Add Terminal Residue" "bar"
(lambda ()
(let ((active-atom (active-residue)))
(if (not active-atom)
(format #t "No active atom~%")
(let ((imol (list-ref active-atom 0))
(chain-id (list-ref active-atom 1))
(res-no (list-ref active-atom 2))
(ins-code (list-ref active-atom 3))
(atom-name (list-ref active-atom 4))
(alt-conf (list-ref active-atom 5)))
(add-terminal-residue imol chain-id res-no "auto" 1))))))
(add-key-binding "Accept Baton Position" "quoteleft" accept-baton-position)