Repository for programs and Python scripts for molecular structure analysis.

See the sub-folders in this repository for specifics. (Sorely need to improve on this.)

Collection of links to launchable Jupyter environment where various structure/function analysis tools work. Many of my recent scripts are built with use in these environments in mind:

• bio3d-binder - launchable, working Jupyter-based environment with the Bio3D package for Macromolecular Structure Analysis running in R+Jupyter (RStudio is an option there, too) with some examples (R-based).

• cl_demo-binder - launchable, working Jupyter-based environment that has a collection of demonstrations of useful resources on command line (or useable in Jupyter sessions) for manipulating structure files.

• PDBmodelComparator - launchable, working Jupyter-based environment that has a collection of demonstrations of resources generating overviews between models of a series of related macromolecular structures available in the Protein Data Bank. If you have two or more models of essentially the same structure and are wondering which one has the information you seek, this tool is for you. It allows you to update the summaries as more related structures are solved. Additionally, it makes a separate summary of which structure has the most of a each chain represented. The information incorporated can be customized with addiitonal knowledge. It allows you to quickly & programmatically update the summaries as more related structures are solved.

• pdbsum-binder - launchable, working Jupyter-based environment that has a collection of demonstrations of my useful resources for analyzing data from PDBsum. The pdbsum-utilities sub-folder in this repo is related as it host many of the scripts and code backing the data analyses.

• PDBrenum - So far I have made a repo here where the main software is already installed and runs the pipeline in sessions served by MyBinder.org. I placed a demonstration notebook demo.ipynb in there in addition to the PDBrenum.ipynb the author's provided. (I actually haven't discerned the purpose of that notebook yet, maybe it is clear in the article?) My demo notebook steps through using it in the sessions. Additionally, I give advice on how you can use PDBrenum.py to map chain IDs in PDB files to UniProt IDs here, relying on the SIFTS data which underlies the PDBrenum.py process, and have expanded that to a demostration notebook, chainID_mapping_to_UniProt_id_demo.ipynb.

• pdbepisa-binder - Analysis of PDBePISA-related data via active Jupyter sessions provided via MyBinder.org. Adapt the demonstrations to analyze your favorite structures.

• pymol-binder

• Python_basics_on_PDB_file

Dockerfiles for Structural Analysis (Structural Bioinformatics) Docker images.

"Learned a handy pair of grep flags - "grep -F -f". I find it useful for grabbing the intersection of two #cryoem particle star files, e.g. from masked classification of different domains. (here particle list is just the rlnImageName column of http://class1.star )" Source

grep -F -f particle_list_class1 class2.star >& class12_instersect.star &

• rna-tools (previously rna-pdb-tools): a toolbox to analyze sequences, structures and simulations of RNA

• PDBrenum: A webserver and program providing PDB renumbered according to their UniProt sequences. The associated scientific article shows how to run it as a Python script in detail. The Announcement.

• Converters provided by GEMMI tools in web browser via web assembly - site can do (More about Gemmi here):

  • PDB ➜ mmCIF
  • mmCIF ➜ PDB
  • mmCIF ➜ MTZ
  • MTZ ➜ mmCIF
  • 2 × data files ➜ mmCIF (deposition-ready)

• bioptools has pdbsplitchains that Split a PDB file into separate files for each chain. (See here.) The package has other scripts with structure-related abilities.

• exploder.py by Tom Peacock here looks to be meant to separate chains in a protein complex for visualization purposes, so you can have a scene where looks like complex pulled apart some like parts manuals often show assemblies in 'exploded view'.

• See more related tools here.

My sequencework repo - for utilities and code dealing with nucleic and protein sequences

My proteomicswork repo - for utilities and code dealing with proteomics analysis