remarks TESTSEL2.INP remarks Test for atom and tag selection using remarks the recursive selection routine SELRPN remarks ++++++++++++++++++++++++++++++++++++++ remarks Axel Brunger, Cambridge, March 1983 rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat end parameter @TOPPAR:param11.pro @TOPPAR:param11.wat end segment name=m1 chain @TOPPAR:toph11.pep sequence ARG PRO ASP PHE CYS LEU end end end segment name=m2 chain @TOPPAR:toph11.pep { READ SEQUENCE FOR m2 DIRECTLY } sequence cys end end end patch disu reference 1 ( atom m1 5 * ) reference 2 ( atom m2 1 * ) end segment name=solv molecule name=TIP3 number=1 end end ! !check error handling ! cons fix=( atom m1 1 * end cons fix=( atom m1 1 ) end cons fix=( atom m1 1 * around 2.0 ) end cons fix=( known ) fix=? end ! coor remarks PTI COORDINATE FILE remarks TEST FOR ATOM AND TAG SELECTION USING remarks THE RECURSIVE SELECTION ROUTINE SELRPN natom 77 1 1 ARG HT1 27.07708 26.62859 -3.07630 M1 1 0.00000 2 1 ARG HT2 27.16302 28.11629 -2.26167 M1 1 0.00000 3 1 ARG N 26.52150 27.41672 -2.68671 M1 1 0.00000 4 1 ARG HT3 25.97541 27.86614 -3.44921 M1 1 0.00000 5 1 ARG CA 25.60287 26.90862 -1.66101 M1 1 0.00000 6 1 ARG CB 24.61046 25.88466 -2.24845 M1 1 0.00000 7 1 ARG CG 25.17139 24.45824 -2.37946 M1 1 0.00000 8 1 ARG CD 24.12352 23.54053 -2.97928 M1 1 0.00000 9 1 ARG NE 23.64449 24.05797 -4.26878 M1 1 0.00000 10 1 ARG HE 22.80914 24.56944 -4.28403 M1 1 0.00000 11 1 ARG CZ 24.29851 23.86324 -5.43228 M1 1 0.00000 12 1 ARG NH1 25.43401 23.15218 -5.47255 M1 1 0.00000 13 1 ARG HH11 25.80707 22.75785 -4.63271 M1 1 0.00000 14 1 ARG HH12 25.90810 23.01601 -6.34243 M1 1 0.00000 15 1 ARG NH2 23.79744 24.37888 -6.53861 M1 1 0.00000 16 1 ARG HH21 22.94682 24.90359 -6.50511 M1 1 0.00000 17 1 ARG HH22 24.26830 24.24498 -7.41059 M1 1 0.00000 18 1 ARG C 26.25638 26.21651 -0.46589 M1 1 0.00000 19 1 ARG O 27.26772 25.51909 -0.61187 M1 1 0.00000 20 2 PRO N 25.66904 26.42017 0.69830 M1 2 0.00000 21 2 PRO CD 24.63936 27.41402 0.96379 M1 2 0.00000 22 2 PRO CA 26.19135 25.80698 1.92573 M1 2 0.00000 23 2 PRO CB 25.36400 26.40813 3.01440 M1 2 0.00000 24 2 PRO CG 24.53110 27.55428 2.47990 M1 2 0.00000 25 2 PRO C 26.24785 24.28339 1.83772 M1 2 0.00000 26 2 PRO O 25.46158 23.66068 1.11164 M1 2 0.00000 27 3 ASP N 27.17664 23.70667 2.57695 M1 3 0.00000 28 3 ASP H 27.79381 24.26256 3.09697 M1 3 0.00000 29 3 ASP CA 27.29893 22.24541 2.63179 M1 3 0.00000 30 3 ASP CB 28.50348 21.85178 3.50474 M1 3 0.00000 31 3 ASP CG 29.77921 21.82889 2.71577 M1 3 0.00000 32 3 ASP OD1 29.87929 22.17090 1.55080 M1 3 0.00000 33 3 ASP OD2 30.75916 21.49547 3.31874 M1 3 0.00000 34 3 ASP C 26.08385 21.48537 3.15454 M1 3 0.00000 35 3 ASP O 25.83397 20.33794 2.76425 M1 3 0.00000 36 4 PHE N 25.34766 22.13344 4.03218 M1 4 0.00000 37 4 PHE H 25.57799 23.05643 4.26747 M1 4 0.00000 38 4 PHE CA 24.18735 21.49495 4.66362 M1 4 0.00000 39 4 PHE CB 23.77361 22.29149 5.88510 M1 4 0.00000 40 4 PHE CG 23.26056 23.67055 5.59363 M1 4 0.00000 41 4 PHE CD1 22.05016 23.81339 5.00206 M1 4 0.00000 42 4 PHE CD2 23.94266 24.79233 5.98042 M1 4 0.00000 43 4 PHE CE1 21.50005 25.09502 4.71385 M1 4 0.00000 44 4 PHE CE2 23.36017 26.08017 5.72515 M1 4 0.00000 45 4 PHE CZ 22.18639 26.20490 5.07838 M1 4 0.00000 46 4 PHE C 23.00620 21.36545 3.70627 M1 4 0.00000 47 4 PHE O 22.03032 20.66125 3.99470 M1 4 0.00000 48 5 CYS N 23.11101 22.04654 2.58873 M1 5 0.00000 49 5 CYS H 23.82536 22.71047 2.49261 M1 5 0.00000 50 5 CYS CA 22.17365 21.82735 1.48223 M1 5 0.00000 51 5 CYS CB 22.34247 22.86057 0.39972 M1 5 0.00000 52 5 CYS SG 22.12032 24.59258 0.90514 M1 5 0.00000 53 5 CYS C 22.20398 20.46100 0.80245 M1 5 0.00000 54 5 CYS O 21.25899 20.08260 0.09890 M1 5 0.00000 55 6 LEU N 23.28940 19.74193 1.02067 M1 6 0.00000 56 6 LEU H 24.02284 20.12312 1.54706 M1 6 0.00000 57 6 LEU CA 23.41457 18.38097 0.48730 M1 6 0.00000 58 6 LEU CB 24.88010 18.07779 0.12865 M1 6 0.00000 59 6 LEU CG 25.59087 19.03078 -0.80516 M1 6 0.00000 60 6 LEU CD1 26.95383 18.47829 -1.14227 M1 6 0.00000 61 6 LEU CD2 24.79288 19.23479 -2.06846 M1 6 0.00000 62 6 LEU C 22.96039 17.22452 1.36393 M1 6 0.00000 63 6 LEU OT1 22.95406 16.06778 0.92698 M1 6 0.00000 64 6 LEU OT2 22.58867 17.54677 2.58817 M1 6 0.00000 65 7 CYS HT1 18.97927 27.81414 -1.15749 M2 1 0.00000 66 7 CYS HT2 20.47128 28.62392 -1.10815 M2 1 0.00000 67 7 CYS N 19.97078 27.74947 -0.85038 M2 1 0.00000 68 7 CYS HT3 20.00656 27.62133 0.18108 M2 1 0.00000 69 7 CYS CA 20.61414 26.60506 -1.50844 M2 1 0.00000 70 7 CYS CB 19.91544 25.34917 -1.03481 M2 1 0.00000 71 7 CYS SG 20.13622 24.92038 0.72014 M2 1 0.00000 72 7 CYS C 20.74779 26.45142 -3.02429 M2 1 0.00000 73 7 CYS OT1 21.37006 25.49785 -3.51538 M2 1 0.00000 74 7 CYS OT2 20.16176 27.39148 -3.74285 M2 1 0.00000 75 8 TIP3 OH2 21.41498 27.23412 -7.18018 SOLV 1 0.00000 76 8 TIP3 H1 21.07276 27.27709 -6.24154 SOLV 1 0.00000 77 8 TIP3 H2 21.06105 28.01167 -7.69994 SOLV 1 0.00000 end ! cons fix=( not known ) end cons fix=(atom m1 1 ht1 or atom %2 1 * ) fix=? end display $select cons fix=( (resn ARG and type C) or (resn PHE and name H )) fix=? end cons fix=(resn ARG : ASP ) fix=? end cons fix=((resid 1) and (type C*) ) fix=? end cons fix=((id 2 : 9) and not id 7 ) fix=? end cons fix=( atom M1 2 C around 3.0 ) fix=? end cons fix=( byres (atom M1 2 C around 3.0) ) fix=? end cons fix=((atom M1 2 C or atom M1 3 H) around 0.5 ) fix=? end cons fix=( point=(2.0 3.0 4.0) cut 35.0 ) fix=? end cons fix=(hydrogen ) fix=? end cons fix=(chemical CH2E ) fix=? end cons fix=( user) end cons fix=( bygroup ( type NH* and resname ARG ) ) fix=? end cons fix=( not all ) end display $select vector ident ( store1 ) ( bygroup ( type NH* and resname ARG ) ) vector show sum ( charge ) ( bygroup ( type NH* and resname ARG ) ) vector show sum ( charge ) ( store1 ) vector show sum ( charge ) ( attribute store1 = 1 ) vector ident ( store2 ) ( id 2 ) vector show sum ( charge ) ( id 2 ) vector show sum ( charge ) ( store2 ) vector show sum ( charge ) ( attribute store2 = 1 ) vector ident ( store9 ) ( id 9 ) vector show sum ( charge ) ( id 9 ) vector show sum ( charge ) ( store9 ) vector show sum ( charge ) ( attribute store9 = 1 ) display $select $result vector show elem ( name ) ( bondedto name N* ) vector show elem ( name ) ( bondedto ( resid 5 and name SG ) ) {* test atom attribute selection *} {* ============================= *} vector show element ( mass ) ( attribute mass gt 30.0 ) vector show element ( charge ) ( attribute charge eq 0.1 ) vector show max ( charge ) ( attribute charge lt 0.1 ) vector show max ( charge ) ( attribute charge gt 0.1 ) vector show max ( charge ) ( attribute charge le 0.1 ) vector show max ( charge ) ( attribute charge ge 0.1 ) vector do ( b = 3.0 ) ( name cb ) vector show element ( b ) ( attribute b eq 3.0 ) vector do ( bcomp = 4.0 ) ( name cb ) vector show element ( bcomp ) ( attribute bcomp eq 4.0 ) vector do ( harm = 5.0 ) ( name cb ) vector show element ( const ) ( attribute harm eq 5.0 ) {* NOW TEST THE LOOP OVER ATOM ID'S *} {* ================================ *} for $1 in id ( resid 1 ) loop main vector show element ( charge ) ( id $1 ) end loop main cons fix=( tag ) fix=? end cons fix=( byresidue ( tag ) ) end {* now test the symmetry around feature *} vector do ( segid="1" ) ( all ) duplicate selection=( segid="1" ) segid="2" end duplicate selection=( segid="1" ) segid="3" end xrefin a=61.4 b=61.4 c=169.8 alpha=90. beta=90. gamma=120. symmetry=(x,y,z) ! Space group symmetry P6(5)22 symmetry=(-y,x-y,z+2/3) symmetry=(-x+y,-x,z+1/3) symmetry=(-x,-y,z+1/2) symmetry=(y,-x+y,z+1/6) symmetry=(x-y,x,z+5/6) symmetry=(y,x,-z+2/3) symmetry=(x-y,-y,-z) symmetry=(-x,-x+y,-z+1/3) symmetry=(-y,-x,-z+1/6) symmetry=(-x+y,y,-z+1/2) symmetry=( x,x-y,-z+5/6 ) end coor fractionalize end coor rotate matrix=( 0 -1 0 ) ( 1 -1 0 ) ( 0 0 1 ) selection=( segid 2 ) end coor translate vector=( 0 1 0.66666 ) selection=( segid 2 ) end coor rotate matrix=( -1 +1 0 ) ( -1 0 0 ) ( 0 0 1 ) selection=( segid 3 ) end coor translate vector=( 1 0 0.33333 ) selection=( segid 3 ) end coor translate vector=( 0.4 0. 0. ) selection=( segid 3 and resid 1 ) end coor orthogonalize end vector show element ( resid ) ( ( segid 2 or segid 3 ) and ( segid 1 saround 0.1 ) ) vector do (chemical="Fe+3") ( segid 3 and resid 1 ) vector show elem ( chemical ) ( chemical "Fe+3" ) vector show elem ( chemical ) ( chemical Fe+3 ) vector do (segid="Ge+3") ( chemical "Fe+3" ) vector show elem ( segid ) ( segid "Ge+3" ) vector show elem ( segid ) ( segid Ge+3 ) vector do (resid="Ke+3") ( chemical "Fe+3" ) vector show elem ( resid ) ( resid "Ke+3" ) vector show elem ( resid ) ( resid Ke+3 ) vector do (name="Le+3") ( chemical "Fe+3" ) vector show elem ( name ) (name "Le+3" ) vector show elem ( name ) ( name Le+3 ) vector do (resname="Le+3") ( chemical "Fe+3" ) vector show elem ( resname ) ( resname "Le+3" ) vector show elem ( resname ) ( resname Le+3 ) vector show elem ( resname ) ( atom "Ge+3" "Ke+3" "Le+3" ) vector show elem ( resname ) ( atom Ge+3 "Ke+3" "Le+3" ) vector show elem ( resname ) ( atom "Ge+3" Ke+3 "Le+3" ) vector show elem ( resname ) ( atom "Ge+3" "Ke+3" Le+3 ) delete selection= ( atom "Ge+3" "Ke+3" "Le+3" ) end xrefin scatter ( name c* ) 1 2 3 4 5 6 7 8 9 imag 10 scatter ( name n* ) 2 3 4 5 6 7 8 9 10 imag 11 end vector show elem ( scatter_a1 ) ( attr scatter_a1 > 0 ) vector show elem ( scatter_a1 ) ( attr scatter_a1 <= 0 ) vector show elem ( scatter_b1 ) ( attr scatter_b1 > 1 ) vector show elem ( scatter_b1 ) ( attr scatter_b1 < 1 ) vector show elem ( scatter_a2 ) ( attr scatter_a2 > 2 ) vector show elem ( scatter_a2 ) ( attr scatter_a2 < 2 ) vector show elem ( scatter_b2 ) ( attr scatter_b2 > 3 ) vector show elem ( scatter_b2 ) ( attr scatter_b2 < 3 ) vector show elem ( scatter_a3 ) ( attr scatter_a3 > 4 ) vector show elem ( scatter_a3 ) ( attr scatter_a3 < 4 ) vector show elem ( scatter_b3 ) ( attr scatter_b3 > 5 ) vector show elem ( scatter_b3 ) ( attr scatter_b3 < 5 ) vector show elem ( scatter_a4 ) ( attr scatter_a4 > 6 ) vector show elem ( scatter_a4 ) ( attr scatter_a4 < 6 ) vector show elem ( scatter_b4 ) ( attr scatter_b4 > 7 ) vector show elem ( scatter_b4 ) ( attr scatter_b4 < 7 ) vector show elem ( scatter_fp ) ( attr scatter_fp > 8 ) vector show elem ( scatter_fp ) ( attr scatter_fp < 8 ) vector show elem ( scatter_fdp ) ( attr scatter_fdp > 9 ) vector show elem ( scatter_fdp ) ( attr scatter_fdp < 9 ) stop