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[ccp4bb]: refmac5 parameter file
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Dear all,
I am trying to create a refmac5 parameter file for a small moleucule known
as enterochelin. I have a pdb file from the cambridge database. I have
tried using sketcher, but I just cannot get it to run without crashing
on me at various points. I am not sure what the final output is supposed
to look like and where it should go.
I have included a copy of the pdb file from the small molecule database.
Following the pdb file, I have included a copy of the ccp4.def file
from sketcher. Note that the oxygens on the benzene rings coordinate a +3
metal (Fe) and are negatively charged; therefore, although they appear to
be too close together, they are not. Also note that the ccp4.def file will
not work if you simply cut and paste it into a file since my mail program
insists on adding carriage returns. Simply join all the lines at the end
of the file starting with:
XY "NULL {-0.525013877304 0.619353079357
and it will work fine.
Any help in constructing an appropriate refmac5 parameter file would be
greatly appreciated.
Thanks,
Dave Goetz
PDB FILE
ATOM 1 O1 ENT 0 76.734 28.890 54.097 0.00 0.00
ATOM 2 O2 ENT 0 75.174 30.712 52.966 0.00 0.00
ATOM 3 O3 ENT 0 77.308 31.441 54.301 0.00 0.00
ATOM 4 O4 ENT 0 75.943 29.347 56.423 0.00 0.00
ATOM 5 O5 ENT 0 73.854 29.985 54.932 0.00 0.00
ATOM 6 O6 ENT 0 75.497 31.947 55.951 0.00 0.00
ATOM 7 O7 ENT 0 79.141 25.550 53.138 0.00 0.00
ATOM 8 O8 ENT 0 73.602 30.757 49.046 0.00 0.00
ATOM 9 O9 ENT 0 80.218 34.297 53.216 0.00 0.00
ATOM 10 O10 ENT 0 81.037 28.344 50.316 0.00 0.00
ATOM 11 O11 ENT 0 78.240 29.550 48.319 0.00 0.00
ATOM 12 O12 ENT 0 79.893 32.293 49.199 0.00 0.00
ATOM 13 O13 ENT 0 77.124 28.697 50.067 0.00 0.00
ATOM 14 O14 ENT 0 78.013 32.093 50.413 0.00 0.00
ATOM 15 O15 ENT 0 79.787 29.680 51.600 0.00 0.00
ATOM 16 N1 ENT 0 78.345 27.555 52.442 0.00 0.00
ATOM 17 N2 ENT 0 75.463 30.729 50.292 0.00 0.00
ATOM 18 N3 ENT 0 79.328 32.266 52.763 0.00 0.00
ATOM 19 C1 ENT 0 77.051 27.937 54.959 0.00 0.00
ATOM 20 C2 ENT 0 73.927 30.356 52.671 0.00 0.00
ATOM 21 C3 ENT 0 77.453 32.607 54.900 0.00 0.00
ATOM 22 C4 ENT 0 76.572 28.172 56.287 0.00 0.00
ATOM 23 C5 ENT 0 73.179 29.970 53.771 0.00 0.00
ATOM 24 C6 ENT 0 76.472 32.873 55.868 0.00 0.00
ATOM 25 C7 ENT 0 76.779 27.217 57.263 0.00 0.00
ATOM 26 C8 ENT 0 71.855 29.561 53.617 0.00 0.00
ATOM 27 C9 ENT 0 76.560 34.013 56.659 0.00 0.00
ATOM 28 C10 ENT 0 77.462 26.042 56.951 0.00 0.00
ATOM 29 C11 ENT 0 71.287 29.578 52.347 0.00 0.00
ATOM 30 C12 ENT 0 77.601 34.904 56.439 0.00 0.00
ATOM 31 C13 ENT 0 77.986 25.811 55.687 0.00 0.00
ATOM 32 C14 ENT 0 72.017 29.965 51.251 0.00 0.00
ATOM 33 C15 ENT 0 78.493 34.699 55.442 0.00 0.00
ATOM 34 C16 ENT 0 77.806 26.774 54.678 0.00 0.00
ATOM 35 C17 ENT 0 73.388 30.355 51.376 0.00 0.00
ATOM 36 C18 ENT 0 78.457 33.516 54.635 0.00 0.00
ATOM 37 C19 ENT 0 78.470 26.567 53.360 0.00 0.00
ATOM 38 C20 ENT 0 74.156 30.645 50.155 0.00 0.00
ATOM 39 C21 ENT 0 79.405 33.399 53.488 0.00 0.00
ATOM 40 C22 ENT 0 78.970 27.484 51.137 0.00 0.00
ATOM 41 C23 ENT 0 76.404 30.815 49.191 0.00 0.00
ATOM 42 C24 ENT 0 80.111 32.051 51.588 0.00 0.00
ATOM 43 C25 ENT 0 80.053 28.541 50.969 0.00 0.00
ATOM 44 C26 ENT 0 77.355 29.623 49.097 0.00 0.00
ATOM 45 C27 ENT 0 79.329 32.216 50.247 0.00 0.00
ATOM 46 C28 ENT 0 77.949 27.500 50.039 0.00 0.00
ATOM 47 C29 ENT 0 77.206 32.074 49.180 0.00 0.00
ATOM 48 C30 ENT 0 80.790 30.715 51.557 0.00 0.00
CCP4.def file
#CCP4I VERSION CCP4Interface 1.2.7
#CCP4I SCRIPT DEF Mol
#CCP4I DATE 14 Jul 2001 16:17:08
#CCP4I USER dgoetz
dimension 3
chem_comp_id ENT
chem_comp_name ""
chem_comp_type ""
nAtoms 48
nH 0
xy,0 ""
Coor,10 "3.9694166667 -1.8666875 -2.4817083333"
Coor,11 "1.1724166667 -0.6606875 -4.4787083333"
Coor,12 "2.8254166667 2.0823125 -3.5987083333"
Coor,13 "0.0564166667 -1.5136875 -2.7307083333"
Coor,14 "0.9454166667 1.8823125 -2.3847083333"
Coor,15 "2.7194166667 -0.5306875 -1.1977083333"
Coor,16 "1.2774166667 -2.6556875 -0.3557083333"
Coor,17 "-1.6045833333 0.5183125 -2.5057083333"
Coor,18 "2.2604166667 2.0553125 -0.0347083333"
Coor,19 "-0.0165833333 -2.2736875 2.1612916667"
Coor,20 "-3.1405833333 0.1453125 -0.1267083333"
Coor,21 "0.3854166667 2.3963125 2.1022916667"
Coor,22 "-0.4955833333 -2.0386875 3.4892916667"
Coor,23 "-3.8885833333 -0.2406875 0.9732916667"
Coor,24 "-0.5955833333 2.6623125 3.0702916667"
Coor,25 "-0.2885833333 -2.9936875 4.4652916667"
Coor,26 "-5.2125833333 -0.6496875 0.8192916667"
Coor,27 "-0.5075833333 3.8023125 3.8612916667"
Coor,28 "0.3944166667 -4.1686875 4.1532916667"
Coor,30 "0.5334166667 4.6933125 3.6412916667"
Coor,29 "-5.7805833333 -0.6326875 -0.4507083333"
Coor,31 "0.9184166667 -4.3996875 2.8892916667"
Coor,32 "-5.0505833333 -0.2456875 -1.5467083333"
Coor,33 "1.4254166667 4.4883125 2.6442916667"
Coor,34 "0.7384166667 -3.4366875 1.8802916667"
Coor,35 "-3.6795833333 0.1443125 -1.4217083333"
Coor,36 "1.3894166667 3.3053125 1.8372916667"
Coor,37 "1.4024166667 -3.6436875 0.5622916667"
Coor,38 "-2.9115833333 0.4343125 -2.6427083333"
Coor,40 "1.9024166667 -2.7266875 -1.6607083333"
Coor,39 "2.3374166667 3.1883125 0.6902916667"
Coor,41 "-0.6635833333 0.6043125 -3.6067083333"
Coor,42 "3.0434166667 1.8403125 -1.2097083333"
Coor,43 "2.9854166667 -1.6696875 -1.8287083333"
Coor,44 "0.2874166667 -0.5876875 -3.7007083333"
Coor,45 "2.2614166667 2.0053125 -2.5507083333"
Coor,46 "0.8814166667 -2.7106875 -2.7587083333"
Coor,47 "0.1384166667 1.8633125 -3.6177083333"
Coor,48 "3.7224166667 0.5043125 -1.2407083333"
Coor,0 ""
Coor,1 "-0.3335833333 -1.3206875 1.2992916667"
Coor,2 "-1.8935833333 0.5013125 0.1682916667"
Coor,3 "0.2404166667 1.2303125 1.5032916667"
Coor,4 "-1.1245833333 -0.8636875 3.6252916667"
Coor,5 "-3.2135833333 -0.2256875 2.1342916667"
Coor,6 "-1.5705833333 1.7363125 3.1532916667"
Coor,7 "2.0734166667 -4.6606875 0.3402916667"
Coor,8 "-3.4655833333 0.5463125 -3.7517083333"
Coor,9 "3.1504166667 4.0863125 0.4182916667"
Name,10 O10
Name,11 O11
Name,12 O12
Name,13 O13
Name,14 O14
Name,15 O15
Name,16 N1
Name,17 N2
Name,18 N3
Name,19 C1
Name,20 C2
Name,21 C3
Name,22 C4
Name,23 C5
Name,24 C6
Name,25 C7
Name,26 C8
Name,27 C9
Name,28 C10
Name,30 C12
Name,29 C11
Name,31 C13
Name,32 C14
Name,33 C15
Name,34 C16
Name,35 C17
Name,36 C18
Name,37 C19
Name,38 C20
Name,40 C22
Name,39 C21
Name,41 C23
Name,42 C24
Name,43 C25
Name,0 ""
Name,44 C26
Name,45 C27
Name,1 O1
Name,46 C28
Name,2 O2
Name,47 C29
Name,3 O3
Name,48 C30
Name,4 O4
Name,5 O5
Name,6 O6
Name,7 O7
Name,8 O8
Name,9 O9
Element,10 O
Element,11 O
Element,12 O
Element,13 O
Element,14 O
Element,15 O
Element,16 N
Element,17 N
Element,18 N
Element,19 C
Element,20 C
Element,21 C
Element,22 C
Element,23 C
Element,24 C
Element,25 C
Element,26 C
Element,27 C
Element,28 C
Element,30 C
Element,29 C
Element,31 C
Element,32 C
Element,33 C
Element,34 C
Element,35 C
Element,36 C
Element,37 C
Element,38 C
Element,40 C
Element,39 C
Element,41 C
Element,42 C
Element,43 C
Element,44 C
Element,45 C
Element,46 C
Element,47 C
Element,48 C
Element,0 C
Element,1 O
Element,2 O
Element,3 O
Element,4 O
Element,5 O
Element,6 O
Element,7 O
Element,8 O
Element,9 O
Type,0 ""
Type,1 no_type
Type,2 no_type
Type,3 no_type
Type,4 no_type
Type,5 no_type
Type,6 no_type
Type,7 no_type
Type,8 no_type
Type,9 no_type
Type,10 no_type
Type,11 no_type
Type,12 no_type
Type,13 no_type
Type,14 no_type
Type,15 no_type
Type,16 no_type
Type,17 no_type
Type,18 no_type
Type,20 no_type
Type,19 no_type
Type,21 no_type
Type,22 no_type
Type,23 no_type
Type,24 no_type
Type,25 no_type
Type,26 no_type
Type,27 no_type
Type,28 no_type
Type,29 no_type
Type,30 no_type
Type,31 no_type
Type,32 no_type
Type,33 no_type
Type,34 no_type
Type,35 no_type
Type,36 no_type
Type,37 no_type
Type,38 no_type
Type,39 no_type
Type,40 no_type
Type,41 no_type
Type,42 no_type
Type,43 no_type
Type,44 no_type
Type,45 no_type
Type,46 no_type
Type,47 no_type
Type,48 no_type
Charge,20 0
Charge,19 0
Charge,21 0
Charge,22 0
Charge,23 0
Charge,24 0
Charge,25 0
Charge,26 0
Charge,27 0
Charge,28 0
Charge,29 0
Charge,30 0
Charge,31 0
Charge,32 0
Charge,33 0
Charge,34 0
Charge,35 0
Charge,36 0
Charge,37 0
Charge,38 0
Charge,39 0
Charge,40 0
Charge,41 0
Charge,42 0
Charge,43 0
Charge,44 0
Charge,45 0
Charge,46 0
Charge,47 0
Charge,48 0
Charge,0 0
Charge,1 -1
Charge,2 -1
Charge,3 -1
Charge,4 -1
Charge,5 -1
Charge,6 -1
Charge,7 0
Charge,8 0
Charge,9 0
Charge,10 0
Charge,11 0
Charge,12 0
Charge,13 0
Charge,14 0
Charge,15 0
Charge,16 0
Charge,17 0
Charge,18 0
nChiral 3
ChiralCentre,0 ""
ChiralCentre,1 C24
ChiralCentre,2 C22
ChiralCentre,3 C23
ChiralNaybrs,0 ""
ChiralNaybrs,1 "N3 C27 C30"
ChiralNaybrs,2 "N1 C25 C28"
ChiralNaybrs,3 "N2 C26 C29"
Chirality,0 +
Chirality,1 +
Chirality,2 +
Chirality,3 +
nBonds 51
Bonds,0 ""
Bonds,1 "1 19"
Bonds,2 "2 20"
Bonds,3 "3 21"
Bonds,4 "4 22"
Bonds,5 "5 23"
Bonds,6 "6 24"
Bonds,7 "7 37"
Bonds,8 "8 38"
Bonds,9 "9 39"
Bonds,10 "10 43"
Bonds,11 "11 44"
Bonds,12 "12 45"
Bonds,13 "13 44"
Bonds,14 "13 46"
Bonds,15 "14 45"
Bonds,16 "14 47"
Bonds,17 "15 43"
Bonds,18 "15 48"
Bonds,19 "16 37"
Bonds,20 "16 40"
Bonds,21 "17 38"
Bonds,22 "17 41"
Bonds,23 "18 39"
Bonds,24 "18 42"
Bonds,25 "19 22"
Bonds,26 "19 34"
Bonds,27 "20 23"
Bonds,28 "20 35"
Bonds,29 "21 24"
Bonds,30 "21 36"
Bonds,31 "22 25"
Bonds,32 "23 26"
Bonds,33 "24 27"
Bonds,34 "25 28"
Bonds,35 "26 29"
Bonds,36 "27 30"
Bonds,37 "28 31"
Bonds,38 "29 32"
Bonds,39 "30 33"
Bonds,40 "31 34"
Bonds,41 "32 35"
Bonds,42 "33 36"
Bonds,43 "34 37"
Bonds,44 "35 38"
Bonds,45 "36 39"
Bonds,46 "40 43"
Bonds,47 "40 46"
Bonds,48 "41 44"
Bonds,49 "41 47"
Bonds,50 "42 45"
Bonds,51 "42 48"
Bondtype,10 2
Bondtype,11 2
Bondtype,12 2
Bondtype,13 1
Bondtype,14 1
Bondtype,15 1
Bondtype,16 1
Bondtype,17 1
Bondtype,18 1
Bondtype,19 1
Bondtype,20 1
Bondtype,21 1
Bondtype,22 1
Bondtype,23 1
Bondtype,24 1
Bondtype,25 1
Bondtype,26 2
Bondtype,27 1
Bondtype,28 2
Bondtype,29 1
Bondtype,30 2
Bondtype,31 2
Bondtype,32 2
Bondtype,33 2
Bondtype,34 1
Bondtype,35 1
Bondtype,36 1
Bondtype,37 2
Bondtype,38 2
Bondtype,39 2
Bondtype,40 1
Bondtype,41 1
Bondtype,42 1
Bondtype,43 1
Bondtype,44 1
Bondtype,45 1
Bondtype,46 1
Bondtype,47 1
Bondtype,48 1
Bondtype,49 1
Bondtype,50 1
Bondtype,51 1
Bondtype,0 ""
Bondtype,1 1
Bondtype,2 1
Bondtype,3 1
Bondtype,4 1
Bondtype,5 1
Bondtype,6 1
Bondtype,7 2
Bondtype,8 2
Bondtype,9 2
nPlane 3
plane,0 ""
plane,1 "C4 C7 C10 C13 C16 C1 C19 O7 O1 O4"
plane,2 "C15 C18 C3 C6 C9 C12 C21 O9 O3 O6"
plane,3 "C5 C2 C17 C14 C11 C8 O5 O2 C20 O8"
filename 1
XY "NULL {-0.525013877304 0.619353079357
-1.69835636417} {1.85189909452 0.364400687004 -0.55043258535}
{0.0128541277191 1.88241352348 0.5363850803} {-0.0935932371782
2.92054250437 -2.57197496601} {2.31817714629 1.83890847469 -2.48550275527}
{1.49988277298 3.59165822414 -0.524503868367} {-3.88095582643
-1.66142880139 -2.88352202624} {4.03677004298 -3.16925122082
0.210653568042} {-1.12650205868 2.10616927572 4.5927210925}
{-3.80673785445 -3.03810932533 1.29549441636} {-0.427800473701
-4.33826354386 1.69303081092} {-0.89511753372 -2.38140006641
4.33559738454} {-0.152006379476 -3.11458149281 -0.16576150011}
{0.439004560929 -1.36568929659 2.84005538625} {-2.38938682651
-1.30976977375 1.29872830661} {-2.18710218674 -1.44479876648
-1.39288851151} {2.13441663024 -2.0518434977 0.59675261411}
{-1.11474116329 0.837218977804 2.71871553681} {-1.38132900644
0.997794101142 -2.63390368668} {2.86007991328 -0.0534188349517
-1.31054329029} {0.261997622819 2.91809166778 1.31399700167}
{-1.12185626192 2.30067448112 -3.16628194537} {3.1381407586 0.780361822367
-2.38105344054} {1.04933983809 3.90780844116 0.70515059696}
{-1.90450790921 2.78158768143 -4.19760579981} {4.16379476436
0.467929329561 -3.27234059848} {1.29966472706 5.10650610238 1.36354741268}
{-2.94553766766 2.0022119764 -4.70088360821} {4.9245137832 -0.675878575509
-3.05138121155} {0.803133434745 5.28370138936 2.64729992233}
{-3.25574016018 0.759024984137 -4.16806702072} {4.66197876648
-1.50561140965 -1.99001238361} {0.126080091284 4.29348366391
3.27401008367} {-2.48697971688 0.251585282171 -3.10535241665}
{3.5924944513 -1.22749175571 -1.08104662097} {-0.185278498342 3.0621114152
2.61158105822} {-2.8998798638 -1.03039800096 -2.46746423645}
{3.27994004678 -2.21150820841 -0.0328165102366} {-0.844587870491
1.97314271826 3.39097847218} {-2.51029087272 -2.65752002465
-0.669322879916} {1.55851755597 -3.01332502416 1.51814912514}
{-1.66448976161 -0.31854550256 3.352690256} {-2.98360860756 -2.36303780295
0.747579566615} {0.230365510168 -3.6023137402 1.04570290005}
{-0.637765887654 -1.46414826595 3.61813779347} {-1.38412084433
-3.64586807111 -0.725981561528} {1.38810578667 -2.4911796858
2.90621615324} {-2.8262210803 -0.911299115112 2.6138252494}"