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#573 CIF read crashes with _geom_bond_distance and no lattice constants

v10
open
nobody
CIF (4)
5
2016-03-04
2016-03-03
Andrius Merkys
No

Jmol crashes while trying to read molecular (_atom_site_Cartn_[xyz] tags and no _cell_length_* or _cell_angle_*) CIF file having _geom_bond_distance tag. I suppose the bug is in the distance measuring code, which tries to generate fractional-to-orthogonal conversion matrix from lattice constants, what is clearly not needed for molecular CIF files. A MWE CIF file is attached.

1 Attachments
ico-no-cell.cif

Discussion

  • Bob Hanson

    Bob Hanson - 2016-03-03

    This is fixed. Also, Jmol will now read CIF files as simple as the following, thus assuming all bonds are single bonds:

    data_icosahedron
    loop_
    atom_site_label
    _atom_site_Cartn_x
    _atom_site_Cartn_y
    _atom_site_Cartn_z
    C01 0.0000000000 0.0000000000 9.5105651630
    C02 8.5065080835 0.0000000000 4.2532540418
    C03 2.6286555606 8.0901699437 4.2532540418
    C04 -6.8819096024 5.0000000000 4.2532540418
    C05 -6.8819096024 -5.0000000000 4.2532540418
    C06 2.6286555606 -8.0901699437 4.2532540418
    C07 6.8819096024 5.0000000000 -4.2532540418
    C08 -2.6286555606 8.0901699437 -4.2532540418
    C09 -8.5065080835 0.0000000000 -4.2532540418
    C10 -2.6286555606 -8.0901699437 -4.2532540418
    C11 6.8819096024 -5.0000000000 -4.2532540418
    C12 0.0000000000 0.0000000000 -9.5105651630
    loop
    _geom_bond_atom_site_label_1
    _geom_bond_atom_site_label_2
    C01 C02
    C01 C03
    C01 C04
    C01 C05
    C01 C06
    C02 C03
    C03 C04
    C04 C05
    C05 C06

     

  • Andrius Merkys

    Andrius Merkys - 2016-03-04

    Thank you very much for the prompt fix!

     

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