Error Importing local pdb from VESTA: ValueError: Cannot parse empty string into integer

[MaxPelly]

Describe the bug
I am trying to import a local pdb structure generated from a cif using VESTA. Both the .pdb and .cif open and display without errors in VESTA however when trying to import the pdb using molecular nodes I get the error shown bellow.

To Reproduce
Steps to reproduce the behavior:

1. Get a cif (eg from ICSD or attached, will need to strip extra .txt extension, github dosent seem to like cifs)
2. Using VESTA convert the cif to a .pdb (or use attached, again remove extra .txt)
3. In blender under the scenes tab find Molecular nodes
4. Under Import select local and locate the .pdb file
5. click local to try and import

Expected behavior
The structure is imported

Error Codes
Please include associated error codes that are shown in the python console when the error occurs.

To view the python console on Windows, Window -> Toggle System Console, on Mac you must start Blender from the terminal.

06:40.969  bpy.rna          | ERROR Python script error in MN_OT_import_local.execute
06:40.969  operator         | ERROR Python: Traceback (most recent call last):
                            |   File "C:\Users\mp250\AppData\Roaming\Blender Foundation\Blender\5.0\extensions\blender_org\molecularnodes\entities\molecule\pdb.py", line 31, in get_structure
                            |     array = pdb.get_structure(
                            |             ^^^^^^^^^^^^^^^^^^
                            |   File "C:\Users\mp250\AppData\Roaming\Blender Foundation\Blender\5.0\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdb\convert.py", line 96, in get_structure
                            |     return pdb_file.get_structure(model, altloc, extra_fields, include_bonds)
                            |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                            |   File "C:\Users\mp250\AppData\Roaming\Blender Foundation\Blender\5.0\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdb\file.py", line 421, in get_structure
                            |     res_id[i] = de



code_hybrid36(line[_res_id])
                            |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                            |   File "src/biotite/structure/io/pdb/hybrid36.pyx", line 158, in biotite.structure.io.pdb.hybrid36.decode_hybrid36
                            | ValueError: Cannot parse empty string into integer

Desktop (please complete the following information):

• OS: Windows 11
• Hardware: x86 PC
• Blender Version: 5.0.1
• MolecularNodes Version: 4.5.10

Additional context
Sr3Ru2O7.pdb.txt
Sr3Ru2O7.cif.txt

[BradyAJohnston]

Because the .pdb file is position-based and VESTA is writing just a space to the position where a res_id is expected we are getting the error. The python library currently used for parsing structures is biotite which is very strict about sticking to spec for parsing files. I'm guessing that having a blank value for res_id is against the spec. If possible I would recommend sticking to .cif instead of .pdb as it has been an officially deprecated format for many years now.

You can get around this import error if you use the MDAnalysis backend by specifying the .pdb for both topology and trajectory and import this will work:

[MaxPelly]

Ahh, cifs would be much better but also seem to have an error, will open a new issue for that though