pdbio | Pandas-based Data Handler for VCF , BED , and SAM Files | Genomics library

The chain name format in _ATOM_FORMAT_STRING is %c, while in this case you have chain named QA.

Chain names in PDB files were traditionally single characters. But there are only so many letters and digits. For ribosome it's necessary to use longer names. The pdb format has space for a second letter -- empty column on the left from the 1-character chain name. Many programs support it, but not all, and this is not part of the official specification.

So you can either use PDB files with 2-character chains (if the rest of your workflow supports it) or rename chains in the output (your output is only a tiny part of the original structure).

Here is how to do it in gemmi:

You were quite close.

But you have to provide a Select class as second argument to io.save. Have a look at the doc comment. It says that this argument should provide accept_model, accept_chain, accept_residue and accept_atom.

I created a class ResidueSelect that inherits from Bio.PDB.PDBIO.Select. That way I only have to override the methods we need. In our case for chain and residues.

Because we only want to save the current residue in the current chain, I provide two respective arguments for the constructor.

retrieve_pdb_file has the optional parameter file_format. When no information is provided, the PDB server returns cif files. Biopython's parser expects a PDB file.

You can change the line to

The error is triggered when BioPython tries to write two-letter chain name using %c format in _ATOM_FORMAT_STRING.

More generally, big structures like 5T2C (ribosome) cannot be written in the traditional PDB format. Many programs and libraries support two-character chain names (written in columns 21-22), but the standard is to have a single-character chain name in column 22. Then you need some extension of atom numbering to support more than 99,999 atoms - the most popular one is hybrid-36.

Anyway, BioPython does not support big PDB files.

(if you write what exactly you want to do someone may be able to suggest another solution)

• In your last loop for atom in residue you are defining the function rotmat every time you loop over an atom but you never call the function.
• Try removing the line def rotmat():
• Currently both your rotation and your translation wouldn't change the atom coordinates.

If you want for example to define C1 as your reference point you could use the following code.

rotation_matrix is just a matrix which does not rotate your protein. np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) would do the same.

In your example you are overwriting all the information about the residue, also the info about the amino acid in the particular position.

Let's increment all ids in our file by 200, loop through the models and structures and then use get_residues() in combination with enumerate to get all the residues and an index.

The residue.id is stored in a list and only the id is changed. This list is then converted back to a tuple and written in place of the original id.