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[Jmol-users] Chemical Component Dictionary - mmCIF reading problem
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From: Rolf H. <rh...@fl...> - 2007-08-31 17:58:55
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Hi,
I tried to read parts of the "PDB Chemical Component Dictionary"
available at the RCSB ("http://deposit.pdb.org/cc_dict_tut.html") in
mmCIF format into Jmol 11.3.11 but no atoms were found.
I extracted for example the record for "CXR" shown below into file
"cxr.cif" and got the following error message:
script ERROR: No atoms found
for file cxr.cif
type cif
----
load >> "cxr.cif" <<
Regards,
Rolf
-------- cxr.cif ---------
data_CXR
#
_chem_comp.id CXR
_chem_comp.name 'CYCLIC ADENOSINE DIPHOSPHATE-RIBOSE'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C15 H21 N5 O13 P2'
_chem_comp.pdbx_synonyms 'CYCLIC ADP-RIBOSE'
_chem_comp.pdbx_formal_charge REL
_chem_comp.pdbx_release_status n
_chem_comp.mon_nstd_flag 541.304
_chem_comp.formula_weight ?
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_ordinal
CXR O2B . O 0 4.779 2.971 3.817 1 1
CXR PB . P 0 5.523 1.657 3.361 1 2
CXR O3A . O 0 5.780 0.737 4.649 1 3
CXR O1B . O 0 6.806 1.706 2.546 1 4
CXR RO5* . O 0 4.499 0.712 2.554 0 5
CXR RC5* . C 0 3.648 1.199 1.488 0 6
CXR RC4* . C 0 2.229 0.682 1.678 0 7
CXR RC3* . C 0 1.678 0.872 3.092 0 8
CXR RO3* . O 0 1.069 2.193 3.311 0 9
CXR RC2* . C 0 0.676 -0.229 3.163 0 10
CXR RO2* . O 0 -0.474 0.185 2.344 0 11
CXR RO4* . O 0 2.200 -0.763 1.485 0 12
CXR RC1* . C 0 1.304 -1.377 2.408 0 13
CXR N1 . N 0 2.142 -2.369 3.176 1 14
CXR C6 . C 0 1.519 -3.203 4.109 1 15
CXR N6 . N 0 0.202 -3.416 4.061 1 16
CXR C5 . C 0 2.373 -3.948 5.042 1 17
CXR N7 . N 0 2.098 -4.884 6.000 1 18
CXR C8 . C 0 3.276 -5.203 6.612 1 19
CXR C2 . C 0 3.569 -2.137 3.292 1 20
CXR N3 . N 0 4.352 -2.806 4.151 1 21
CXR C4 . C 0 3.792 -3.701 5.063 1 22
CXR N9 . N 0 4.310 -4.506 6.029 1 23
CXR C1* . C 0 5.722 -4.583 6.472 1 24
CXR O4* . O 0 6.064 -3.216 6.895 1 25
CXR C2* . C 0 6.686 -4.993 5.406 1 26
CXR O2* . O 0 7.086 -6.311 5.670 1 27
CXR C3* . C 0 7.895 -4.115 5.636 1 28
CXR O3* . O 0 8.697 -3.928 4.422 1 29
CXR C4* . C 0 7.383 -2.839 6.338 1 30
CXR C5* . C 0 7.309 -1.591 5.459 1 31
CXR O5* . O 0 7.107 -0.473 6.334 1 32
CXR PA . P 0 6.931 1.040 5.798 1 33
CXR O2A . O 0 6.257 1.856 6.932 1 34
CXR O1A . O 0 8.230 1.526 5.178 1 35
CXR H2* . H 0 ? ? ? 1 36
CXR H1 . H 0 ? ? ? 1 37
CXR H3* . H 0 ? ? ? 1 38
CXR H2 . H 0 ? ? ? 1 39
CXR H4* . H 0 ? ? ? 1 40
CXR H1* . H 0 ? ? ? 1 41
CXR H3 . H 0 ? ? ? 1 42
CXR H8 . H 0 ? ? ? 1 43
CXR H4 . H 0 ? ? ? 1 44
CXR H5 . H 0 ? ? ? 1 45
CXR 1H5* . H 0 ? ? ? 0 46
CXR 2H5* . H 0 ? ? ? 0 47
CXR H1A . H 0 ? ? ? 1 48
CXR H1B . H 0 ? ? ? 1 49
CXR 1H1 . H 0 ? ? ? 0 50
CXR 2H1 . H 0 ? ? ? 0 51
CXR H6 . H 0 ? ? ? 1 52
CXR H7 . H 0 ? ? ? 1 53
CXR H9 . H 0 ? ? ? 1 54
CXR H10 . H 0 ? ? ? 1 55
CXR HN6 . H 0 ? ? ? 1 56
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
CXR O2B PB DOUB 1
CXR PB O3A SING 2
CXR PB O1B SING 3
CXR PB RO5* SING 4
CXR O3A PA SING 5
CXR O1B H1B SING 6
CXR RO5* RC5* SING 7
CXR RC5* RC4* SING 8
CXR RC5* 1H1 SING 9
CXR RC5* 2H1 SING 10
CXR RC4* RC3* SING 11
CXR RC4* H4* SING 12
CXR RC4* RO4* SING 13
CXR RC3* RC2* SING 14
CXR RC3* H3* SING 15
CXR RC3* RO3* SING 16
CXR RO3* H2 SING 17
CXR RC2* RO2* SING 18
CXR RC2* H1 SING 19
CXR RC2* RC1* SING 20
CXR RO2* H2* SING 21
CXR RO4* RC1* SING 22
CXR RC1* H1* SING 23
CXR RC1* N1 SING 24
CXR N1 C2 SING 25
CXR N1 C6 SING 26
CXR C6 C5 SING 27
CXR C6 N6 DOUB 28
CXR N6 HN6 SING 29
CXR C5 C4 DOUB 30
CXR C5 N7 SING 31
CXR N7 C8 DOUB 32
CXR C8 H8 SING 33
CXR C8 N9 SING 34
CXR C2 H3 SING 35
CXR C2 N3 DOUB 36
CXR N3 C4 SING 37
CXR C4 N9 SING 38
CXR N9 C1* SING 39
CXR C1* H4 SING 40
CXR C1* O4* SING 41
CXR C1* C2* SING 42
CXR O4* C4* SING 43
CXR C2* C3* SING 44
CXR C2* H9 SING 45
CXR C2* O2* SING 46
CXR O2* H10 SING 47
CXR C3* C4* SING 48
CXR C3* H6 SING 49
CXR C3* O3* SING 50
CXR O3* H7 SING 51
CXR C4* H5 SING 52
CXR C4* C5* SING 53
CXR C5* 1H5* SING 54
CXR C5* 2H5* SING 55
CXR C5* O5* SING 56
CXR O5* PA SING 57
CXR PA O2A DOUB 58
CXR PA O1A SING 59
CXR O1A H1A SING 60
#
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