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project-gemmi / gemmi

macromolecular crystallography library and utilities
https://project-gemmi.github.io/
Mozilla Public License 2.0
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got zero models from mmcif written from pymol selection, expected one model #327

Closed diogomart closed 3 months ago

diogomart commented 3 months ago

Hello,

The mmcif attached below, written from pymol, parses to a structure with zero models. Expected one model. Parsing the same file with prody results in a data structure with a model. Reading it again with pymol displays the atoms.

>>> g = gemmi.read_structure("from_pymol.cif")
>>> print(g)

<gemmi.Structure 4fkg with 0 model(s)>
from_pymol.cif ``` # generated by PyMOL 2.5.0 # data_4fkg _entry.id 4fkg # _cell.entry_id 4fkg _cell.length_a 53.305 _cell.length_b 71.634 _cell.length_c 72.407 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _symmetry.entry_id 4fkg _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . LYS A 1 89 ? 9.327 -12.007 -23.312 1.00 24.18 0 A 1 ATOM 2 C CA . LYS A 1 89 ? 10.222 -12.541 -24.329 1.00 24.85 0 A 1 ATOM 3 C C . LYS A 1 89 ? 11.629 -11.974 -24.179 1.00 26.62 0 A 1 ATOM 4 O O . LYS A 1 89 ? 12.596 -12.735 -24.287 1.00 28.52 0 A 1 ATOM 5 C CB . LYS A 1 89 ? 9.650 -12.338 -25.738 1.00 27.40 0 A 1 ATOM 6 C CG . LYS A 1 89 ? 10.520 -12.948 -26.839 1.00 45.43 0 A 1 ATOM 7 C CD . LYS A 1 89 ? 9.934 -12.790 -28.223 1.00 53.19 0 A 1 ATOM 8 C CE . LYS A 1 89 ? 10.829 -13.380 -29.280 1.00 60.75 0 A 1 ATOM 9 N NZ . LYS A 1 89 ? 10.245 -13.221 -30.635 1.00 70.50 0 A 1 ATOM 10 N N . MET A 1 91 ? 13.037 -10.911 -21.352 1.00 23.41 0 A 1 ATOM 11 C CA A MET A 1 91 ? 13.690 -11.518 -20.194 0.50 22.27 0 A 1 ATOM 12 C CA B MET A 1 91 ? 13.613 -11.530 -20.150 0.50 22.36 0 A 1 ATOM 13 C C . MET A 1 91 ? 14.171 -12.922 -20.522 1.00 28.37 0 A 1 ATOM 14 O O . MET A 1 91 ? 15.281 -13.300 -20.106 1.00 28.74 0 A 1 ATOM 15 C CB A MET A 1 91 ? 12.770 -11.531 -19.000 0.50 23.07 0 A 1 ATOM 16 C CB B MET A 1 91 ? 12.526 -11.668 -19.073 0.50 23.32 0 A 1 ATOM 17 C CG A MET A 1 91 ? 12.679 -10.187 -18.344 0.50 24.33 0 A 1 ATOM 18 C CG B MET A 1 91 ? 12.302 -10.389 -18.267 0.50 24.99 0 A 1 ATOM 19 S SD A MET A 1 91 ? 12.088 -10.379 -16.674 0.50 27.44 0 A 1 ATOM 20 S SD B MET A 1 91 ? 10.663 -10.192 -17.478 0.50 27.98 0 A 1 ATOM 21 C CE A MET A 1 91 ? 10.473 -10.990 -17.025 0.50 23.02 0 A 1 ATOM 22 C CE B MET A 1 91 ? 10.250 -11.739 -17.208 0.50 26.08 0 A 1 ATOM 23 N N . ASP A 1 92 ? 13.369 -13.700 -21.272 1.00 24.93 0 A 1 ATOM 24 C CA . ASP A 1 92 ? 13.742 -15.057 -21.682 1.00 26.20 0 A 1 ATOM 25 C C . ASP A 1 92 ? 15.001 -14.994 -22.553 1.00 32.66 0 A 1 ATOM 26 O O . ASP A 1 92 ? 15.937 -15.789 -22.346 1.00 34.34 0 A 1 ATOM 27 C CB . ASP A 1 92 ? 12.593 -15.729 -22.466 1.00 28.34 0 A 1 ATOM 28 C CG . ASP A 1 92 ? 11.437 -16.264 -21.632 0.80 35.60 0 A 1 ATOM 29 O OD1 . ASP A 1 92 ? 11.559 -16.293 -20.383 1.00 36.22 0 A 1 ATOM 30 O OD2 . ASP A 1 92 ? 10.386 -16.598 -22.221 0.80 38.42 0 A 1 ```
wojdyr commented 3 months ago

Hi, it was just fixed this month in #325

diogomart commented 3 months ago

Awesome. Sorry for the duplication.