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Re: [Jmol-users] Chemical Component Dictionary - mmCIF reading problem
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From: Bob H. <ha...@st...> - 2007-08-31 19:47:28
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interesting idea to read these files. Currently Jmol does not support this.
Rolf Huehne wrote:
> 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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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