User:Wayne Decatur/Structure analysis tools: Difference between revisions
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m add another link to pymol-binder |
m link to more of my stuff |
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* [https://www.ebi.ac.uk/complexportal/complex/search?query=*&species=Saccharomyces%20cerevisiae%20(strain%20ATCC%20204508%20%2F%20S288c)&page=1 S. cerevisiae complexes] | * [https://www.ebi.ac.uk/complexportal/complex/search?query=*&species=Saccharomyces%20cerevisiae%20(strain%20ATCC%20204508%20%2F%20S288c)&page=1 S. cerevisiae complexes] | ||
==Compare Related Structures== | |||
* [https://github.com/fomightez/pdbsum-binder Collection of notebooks to analyze PDBsum-derived data using Jupyter/Python] - currently the most prominent feature here facilitates highlighting differences and smiliarites in protein-protein interaction of the same protein pairs in '''different''', related macromolecular complexes. For example, structures solved with different ligands or substrates or structures that share subsets of the same components. | |||
* [https://github.com/fomightez/structurework/tree/master/pdbsum_utilities PDBsum-utilities] - where I share my code to analyze PDBsum-derived data using Python. | |||
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* see also on [https://github.com/fomightez/structurework this page] 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use | * see also on [https://github.com/fomightez/structurework this page] 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use | ||
* click `launch binder` [https://github.com/fomightez/cl_demo-binder here] for a series of demonstrations of useful resources on command line for manipulating structure files. | * click `launch binder` [https://github.com/fomightez/cl_demo-binder here] for a series of demonstrations of useful resources on command line for manipulating structure files. | ||
* [https://github.com/fomightez/structurework/tree/master/pdbsum_utilities PDBsum-utilities] - where I share my code to analyze PDBsum-derived data using Python. | |||
- [pdbsum-binder](https://github.com/fomightez/pdbsum-binder) - working with data from PDBsum integrated with Jupyter/Python | |||
- [jupyter-jsmol-binder](https://github.com/fomightez/jupyter-jsmol-binder) - JMol Jsmol applets in Jupyter notebook | |||
- [Jupyter-desktop_with_pymo](https://github.com/fomightez/Jupyter-desktop_with_pymol) - PyMol graphical user interface served via MyBinder.org | |||
- [pymol-binder](https://github.com/fomightez/pymol-binder) - PyMOL running headless for command line/scripting and interaction with Python. | |||
- [modelit-binder](https://github.com/fomightez/modelit-binder) - Model.it software to produce a 3D model of DNA in bent confirmation combined with Jupyter ecosystem and PyMOL served via MyBinder.org | |||
- [AnimatePymolWithJmol](https://github.com/fomightez/AnimatePymolWithJmol) - Easily animate PyMOL session scenes with Jmol to create an animated GIFs | |||
==R-based utilities== | ==R-based utilities== | ||
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* My [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | * My [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | ||
==Jmol/Jsmol use in Jupyter environments== | |||
* [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder] - My current resource consolidating my efforts to use Jsmol applets in Jupyter and to take advantage of a Jupyter extension made by others to also do that. Jsmol applets directly used in Jupyter are shown [https://nbviewer.jupyter.org/github/fomightez/jupyter-jsmol-binder/blob/master/Jmol%20Jsmol%20applets%20working%20in%20Jupyter%20notebooks.ipynb here]; you can run that notebook actively inside the [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder]. | |||
==References== | ==References== | ||
