Are cif Documents from Structure and read directly from filesystem equal?

[hlvlad]

Hi,

I would like to ask, whether data from original cif file is preserved, when we read_structure(). If it is, how can we access it?

block1 = gemmi.read_structure('./3gqc.cif').make_mmcif_document().sole_block()
block1.get_mmcif_category('_pdbx_unobs_or_zero_occ_residues')
# output: empty dict

vs

block2 = gemmi.cif.read('./3gqc.cif').sole_block()
block2.get_mmcif_category('_pdbx_unobs_or_zero_occ_residues')
# output: dict with actual data

Edit:
Actually

len(list(block1))
# output: 48
len(list(block2))
# output: 238

Can we create structure from cif document, modify it (say delete some residues) and save new cif with all values of original cif present?

[wojdyr]

To preserve Document you can read the structure in two steps:

doc = gemmi.cif.read('./3gqc.cif')
structure = gemmi.make_structure_from_block(doc[0])

The same is done internally in read_structure(), except that Document is not preserved.
(Update 2023: you can call read_structure() with option save_doc to preserve Document.)

Then, after changing the structure, you can modify only selected categories in cif:

groups = gemmi.MmcifOutputGroups(False)  # False -> start with all groups disabled
groups.atoms = True  # enable _atom_site and _atom_site_anisotrop
structure.update_mmcif_block(doc[0], groups)

[lobnaOmar20]

st = gemmi.read_structure('supercell_i00002_w8.cif')
st
<gemmi.Structure # with 0 model(s)>

why gemmi.Structure says 0 models ??

I tried this instead

doc = gemmi.cif.read('supercell_i00002_w8.cif')
structure = gemmi.make_structure_from_block(doc[0])

for neighbor search
ns = gemmi.NeighborSearch(doc[0], 1.8)#.populate(include_h=false)

to get this

TypeError Traceback (most recent call last)
Input In [91], in <cell line: 1>()
----> 1 ns = gemmi.NeighborSearch(doc[0], 1.8)

TypeError: init(): incompatible constructor arguments. The following argument types are supported:
1. gemmi.NeighborSearch(model: gemmi.Model, cell: gemmi.UnitCell, max_radius: float)
2. gemmi.NeighborSearch(st: gemmi.Structure, max_radius: float, model_index: int = 0)
3. gemmi.NeighborSearch(small_structure: gemmi.SmallStructure, max_radius: float)

Invoked with: <gemmi.cif.Block #>, 1.8

[wojdyr]

st = gemmi.read_structure('supercell_i00002_w8.cif')
st
<gemmi.Structure # with 0 model(s)>

why gemmi.Structure says 0 models ??

I suppose that this file is not an mmCIF file with coordinates.

[lobnaOmar20]

it is just a cif file with atomic positions for 114 atoms.

[wojdyr]

then use function read_small_structure
see https://gemmi.readthedocs.io/en/latest/mol.html#small-molecules

[lobnaOmar20]

thank you so much for the quick reply.