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Coot

3,592 bytes added, 12:40, 20 June 2012
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Q: There is the --auto <filename> commandline option for auto-reading mtz files (mtz file has the default labels FWT, PHWT). Can this be made to work with a SHELXE .phs output file after converting with convert2mtz ? - the resulting MTZ file has labels F PHI FOM.
A: use : coot --python -c 'make_and_draw_map("sad.mtz", "F", "PHI", "FOM", "/HKL_base/HKL_base/FOM",1, 0)'  == NCS Rotamer differences == Show me where NCS-related side-chains have different rotamers  (define (compare-ncs-rotamer imol chain-A chain-B) (let ((n-residues (chain-n-residues chain-A imol)) (mismatched-rotamers '())) (for-each (lambda (serial-number) (let ((res-name-A (resname-from-serial-number imol chain-A serial-number)) (res-no-A (seqnum-from-serial-number imol chain-A serial-number)) (ins-code-A (insertion-code-from-serial-number imol chain-A serial-number)) (res-name-B (resname-from-serial-number imol chain-A serial-number)) (res-no-B (seqnum-from-serial-number imol chain-A serial-number)) (ins-code-B (insertion-code-from-serial-number imol chain-A serial-number))) (if (not (= res-no-A res-no-B)) (begin (format #t "sequence number for ~s do not match~%" res-no-A)) (if (not (string=? res-name-A res-name-B)) (begin (format #t "residue names for ~s do not match~%" res-no-A)) (let ((rot-name-A (get-rotamer-name imol chain-A res-no-A ins-code-A)) (rot-name-B (get-rotamer-name imol chain-B res-no-B ins-code-B))) (if (not (string=? rot-name-A rot-name-B)) (begin (format #t "mismatch rotamers ~s ~s~%" rot-name-A rot-name-B) (set! mismatched-rotamers (cons (list imol chain-A res-no-guanoA ins-code-A res-name-A (if (string=? rot-name-A "") "-" rot-name-A) (if (string=? rot-name-B "") "-" rot-name-B)) mismatched-rotamers)))) ))))) (range n-residues)) (dialog-box-of-buttons "Mismatched Rotamers" (cons 300 300) (map (lambda(rotamer) (let ((label (string-append " " (list-ref rotamer 1) " " (number->string (list-ref rotamer 2)) (list-ref rotamer 3) " " (list-ref rotamer 4) ;; res-name ": " (list-ref rotamer 5) " vs. " (list-ref rotamer 6))) (thunk (lambda () (set-go-to-atom-molecule imol) (set-go-to-atom-chain-residue-atom-name (list-ref rotamer 1) (list-ref rotamer 2) " CA ")))) (list label thunk))) mismatched-rotamers) " Close ")))   And one would use this something like:  ;; example usage: (let ((imol (read-pdb "test.pdb"))) (compare-ncs-rotamer imol "A" "B"))
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