Hello
I have tried to upload a .cif-File. Only an error message appeared:
“Could not parse uploaded file. If this seems like a bug, please report it. Crystal Toolkit understands all crystal structure file types and molecule file types supported by pymatgen.”
How can I upload a .cif-File?
Thanks in advance
Hi @mkhorton
I have tried two different structures
First structure:
# CIF file generated by openbabel 3.0.0, see http://openbabel.sf.net
data_I
_chemical_name_common ''
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Mg0 Mg -2.01731 1.58051 0.28654 1.000
O1 O -1.73276 -0.11750 1.55691 1.000
C2 C -2.16639 -1.36746 1.05232 1.000
C3 C -2.05791 -0.06401 2.93956 1.000
O4 O -0.77788 0.64712 -1.14983 1.000
C5 C 0.35636 -0.08425 -0.71608 1.000
C6 C -0.60951 1.13651 -2.47069 1.000
O7 O -0.34605 2.54724 1.16292 1.000
C8 C 0.89368 2.67616 0.49477 1.000
C9 C -0.13123 2.47580 2.55657 1.000
O10 O -2.29179 3.29541 -0.94726 1.000
C11 C -1.44592 4.42870 -0.85050 1.000
C12 C -2.90870 3.27181 -2.22173 1.000
O13 O -3.22545 2.47071 1.76788 1.000
C14 C -3.40213 3.87290 1.74131 1.000
C15 C -4.41092 1.82555 2.20126 1.000
O16 O -3.71877 0.63918 -0.58631 1.000
C17 C -3.59762 -0.32918 -1.61826 1.000
C18 C -4.92140 1.37579 -0.75274 1.000
H19 H -2.11700 0.96439 3.30879 1.000
H20 H -1.25601 -0.56018 3.52702 1.000
H21 H -3.04311 -0.52512 3.18341 1.000
H22 H -1.63952 -1.61089 0.11868 1.000
H23 H -3.26786 -1.38939 0.91677 1.000
H24 H -1.86535 -2.20547 1.72324 1.000
H25 H 0.17804 0.59204 -3.04200 1.000
H26 H -0.33238 2.20471 -2.47521 1.000
H27 H -1.52251 0.94969 -3.06200 1.000
H28 H 0.38569 -0.12717 0.38781 1.000
H29 H 1.31623 0.38265 -1.03125 1.000
H30 H 0.30406 -1.12547 -1.09831 1.000
H31 H 0.63680 3.20835 2.89623 1.000
H32 H -1.03594 2.81449 3.09247 1.000
H33 H 0.18688 1.45632 2.85736 1.000
H34 H 0.74828 2.64901 -0.59301 1.000
H35 H 1.61310 1.88001 0.78689 1.000
H36 H 1.33068 3.67951 0.69191 1.000
H37 H -2.01589 5.36043 -1.06546 1.000
H38 H -0.56951 4.34745 -1.52707 1.000
H39 H -1.08320 4.57539 0.17706 1.000
H40 H -3.19583 2.25485 -2.49596 1.000
H41 H -3.82710 3.89624 -2.20929 1.000
H42 H -2.22858 3.59713 -3.04223 1.000
H43 H -3.89757 4.20328 0.80609 1.000
H44 H -3.99601 4.23093 2.61369 1.000
H45 H -2.42569 4.36906 1.87912 1.000
H46 H -5.73772 0.90228 -0.16853 1.000
H47 H -4.77829 2.41253 -0.40635 1.000
H48 H -5.25388 1.48195 -1.81047 1.000
H49 H -3.72847 0.09288 -2.63733 1.000
H50 H -2.60688 -0.80116 -1.61695 1.000
H51 H -4.32584 -1.15113 -1.44745 1.000
H52 H -4.42028 0.77663 1.85398 1.000
H53 H -5.33912 2.30814 1.82034 1.000
H54 H -4.43750 1.80099 3.31133 1.000
Second structure:
# CIF file generated by openbabel 3.0.0, see http://openbabel.sf.net
data_I
_chemical_name_common ''
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
B0 B -2.58909 -0.51262 0.21715 1.000
O1 O -1.17512 -0.60759 0.74738 1.000
O2 O -2.65235 0.09453 -1.16859 1.000
O3 O -3.40805 0.27028 1.20719 1.000
C4 C -3.60634 -0.38611 2.45352 1.000
C5 C -0.17464 0.14919 0.07845 1.000
C6 C -3.44705 1.26171 -1.32711 1.000
O7 O -3.16401 -1.89448 0.12086 1.000
C8 C -2.39253 -2.79362 -0.66161 1.000
C9 C -2.80918 2.11885 -2.43683 1.000
H10 H -3.43882 1.91087 -0.42411 1.000
C11 C -4.90531 0.88132 -1.67110 1.000
C12 C 1.12494 -0.67814 0.07498 1.000
C13 C 0.02060 1.51191 0.77609 1.000
H14 H -0.39917 0.32351 -0.99404 1.000
C15 C -3.28647 -3.36406 -1.77645 1.000
C16 C -1.83199 -3.89648 0.25732 1.000
H17 H -1.52791 -2.30903 -1.17452 1.000
C18 C -5.08791 -0.79864 2.58083 1.000
C19 C -3.17989 0.56986 3.58168 1.000
H20 H -2.98526 -1.30739 2.57450 1.000
F21 F -5.91110 0.30922 2.48033 1.000
F22 F -5.31679 -1.42111 3.79504 1.000
F23 F -5.42307 -1.68600 1.57562 1.000
F24 F -3.91108 1.74372 3.53012 1.000
F25 F -1.84173 0.87892 3.44432 1.000
F26 F -3.36078 -0.02171 4.81933 1.000
F27 F -2.86117 -4.57373 0.88757 1.000
F28 F -1.02126 -3.33422 1.22586 1.000
F29 F -1.07639 -4.79860 -0.47021 1.000
F30 F -4.38629 -4.00950 -1.23885 1.000
F31 F -2.57782 -4.25569 -2.56206 1.000
F32 F -3.73084 -2.33443 -2.58368 1.000
F33 F 1.52629 -0.96397 1.36827 1.000
F34 F 2.13901 0.00639 -0.57150 1.000
F35 F 0.91618 -1.87093 -0.59233 1.000
F36 F 0.42086 1.33662 2.08815 1.000
F37 F -1.16188 2.22595 0.76825 1.000
F38 F 0.97927 2.25884 0.11494 1.000
F39 F -4.95455 0.13893 -2.83693 1.000
F40 F -5.67507 2.01928 -1.83357 1.000
F41 F -5.46123 0.13256 -0.65218 1.000
F42 F -1.51812 2.45985 -2.07790 1.000
F43 F -3.52703 3.28636 -2.62747 1.000
F44 F -2.76173 1.41796 -3.62927 1.000
Thanks for your help
Leonie
Thanks @Leonie, I’ll look into it. Just taking a quick glance I suspect the issue is that these CIF files do not contain any information about the crystal lattice, so may be out of spec. Whether in spec or not, this would be the reason pymatgen is failing to parse them. In general, CIF files are meant to store crystallographic information (the ‘C’ in CIF), and I haven’t seen them storing just isolated molecules previously. It could be that this is completely valid and we just need to fix the pymatgen implementation. You could also try exporting as .xyz
Thanks for the answer!
I’ve tried to upload the .xyz file. It worked but the preview of the material looks not identical to the created file.
The file was original created with Avogadro and exported from a cml-file to a .xyz-file.
Why ist there such a big difference between the two molecules?
Hi @Leonie,
The difference is due to a bug in the bonding algorithm for molecules (which has been fixed but not deployed to the website yet).
Note that the atomic positions are correct and the same between both. The xyz file does not contain information on which atoms are bonded to which other atoms, so we have to work that out. There are many algorithms in pymatgen which try to answer the question of if two atoms are bonded. Unfortunately, the ones for molecules had a bug where atom labels were permuted leading to the wacky bonds shown. As mentioned, this has been fixed in pymatgen, and will be fixed on the next update to the website too.
Best,
Matt
