Question 1

How to extract chain A from a PDB file using pdb-tools?

Accepted Answer

Use the command 'pdb_selchain -A input.pdb > output.pdb'. This tool selects specific chains and can be piped with others, like 'pdb_tidy', for more complex workflows as shown in the README examples.

Question 2

Can pdb-tools handle mmCIF to PDB conversion?

Accepted Answer

Yes, pdb-tools includes converters for mmCIF to PDB format, but it has limitations on file size and does not support very large molecules with over 99999 atoms or 9999 residues per chain, as noted in the documentation.

Question 3

pdb-tools vs Biopython: which is better for PDB manipulation?

Accepted Answer

pdb-tools is better for quick, dependency-free command-line tasks like chain extraction or renumbering, while Biopython offers a comprehensive library for scripting and numerical analysis but requires more setup and coding expertise.

Question 4

How to install pdb-tools on Windows?

Accepted Answer

Install via pip with 'pip install pdb-tools'. On Windows, the tools have .exe extensions, and the same command-line interface works in the command prompt, ensuring cross-platform usability as mentioned in the README.

Question 5

What are the size limits for files in pdb-tools?

Accepted Answer

pdb-tools does not support mmCIF files with more than 99999 atoms or 9999 residues in a single chain, as stated in the README under limitations, which can be a constraint for large structural datasets.

Question 6

How to renumber residues starting from 1 in pdb-tools?

Accepted Answer

Use 'pdb_reres -1 input.pdb > output.pdb' to renumber residues starting from 1, as demonstrated in the README examples, ensuring consistent numbering for analysis or publication.

pdb-tools

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