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https://github.com/fomightez/structurework

programs and scripts for molecular structure analysis
https://github.com/fomightez/structurework

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programs and scripts for molecular structure analysis

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structurework

=============



Repository for programs and [Python scripts](https://github.com/fomightez/structurework/tree/master/python_scripts) for molecular structure analysis.



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



Related 'Binderized' Utilities

----------------------------



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](https://github.com/fomightez/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](https://github.com/fomightez/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.



- [pdbsum-binder](https://github.com/fomightez/pdbsum-binder) - launchable, working Jupyter-based environment that has a collection of demonstrations of my useful resources for analyzing data from [PDBsum](http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html). The [pdbsum-utilities sub-folder in this repo](https://github.com/fomightez/structurework/tree/master/pdbsum_utilities) is related as it host many of the scripts and code backing the data analyses.



- [PDBrenum](https://github.com/fomightez/PDBrenum) - So far I have made a repo [here](https://github.com/fomightez/PDBrenum) 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](https://www.biostars.org/p/9540519/#9540582), 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`.



- [pymol-binder](https://github.com/fomightez/pymol-binder)



- [Python_basics_on_PDB_file](https://github.com/fomightez/Python_basics_on_PDB_file)



Related 'Docker-ized' Utilities

-------



[Dockerfiles for Structural Analysis (Structural Bioinformatics) Docker images](https://github.com/fomightez/Dockerfiles#dockerfiles-for-structural-analysis-structural-bioinformatics-docker-images).



Related non-Python tips

-----------------------



>"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](https://twitter.com/OliBClarke/status/1100400145286524928)



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



Related resources by others

---------------------------



- [rna-tools (previously rna-pdb-tools): a toolbox to analyze sequences, structures and simulations of RNA](https://github.com/mmagnus/rna-tools/blob/master/index-of-tools.md)



- [PDBrenum: A webserver and program providing PDB renumbered according to their UniProt sequences](http://dunbrack3.fccc.edu/PDBrenum/). The [associated scientific article](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253411) shows how to run it as a Python script in detail. The [Announcement](https://twitter.com/RolandDunbrack/status/1412675616156098562).



- [Converters provided by GEMMI tools in web browser via web assembly](https://project-gemmi.github.io/wasm/) - site can do (More about [Gemmi here](https://github.com/project-gemmi/gemmi)):

    - PDB ➜ mmCIF

    - mmCIF ➜ PDB

    - mmCIF ➜ MTZ

    - MTZ ➜ mmCIF

    - 2 × data files ➜ mmCIF (deposition-ready)



- [bioptools](https://github.com/ACRMGroup/bioptools) has [pdbsplitchains](https://github.com/ACRMGroup/bioptools#pdbsplitchains) that Split a PDB file into separate files for each chain. (See [here](https://www.biostars.org/p/9513505/#9513508).) The package has other scripts with structure-related abilities.



- `exploder.py` by Tom Peacock [here](https://github.com/tp-peacock/pdbTools) 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](https://github.com/fomightez/structurework/tree/master/python_scripts#related-resources-by-others).



See also

--------



[My sequencework repo](https://github.com/fomightez/sequencework/) - for utilities and code dealing with nucleic and protein sequences



[My proteomicswork repo](https://github.com/fomightez/proteomicswork/) - for utilities and code dealing with proteomics analysis