tl;dr:
Click any launch model.it
badge on this page to run automated version of model.it with structure visualization inside your browser.
model.it: software to produce a 3D model of DNA in bent confirmation.
Model.it software to produce a 3D model of DNA in bent confirmation combined with Jupyter ecosystem and PyMOL served via MyBinder.org
Automated running of model.it software to produce a 3D model of DNA in bent confirmation combined with the power of the Jupyter ecosystem and structure visualizations by PyMOL served via MyBinder.org.
If you are just trying to get a PDB file for models of a few sequences, go to the the model.it Server.
This repository is for automated processing of sequences through the model.it server inside your browser in a Jupyter environment provided by MyBinder.org and pipelining that to PyMOL to produce structure visualizations. The PyMOL images will be colored to reflect curvature and bendability if bendIt data is provided from results run through the bendit-binder pipeline.
If you are just interested in using PyMOL in a Jupyter system, go here.
The necesary software will be installed already in each active session launched from this repo.
The model.it authors request users cite:
Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena.
Munteanu, M. G., Vlahovicek, K., Parthasaraty, S., Simon, I. and Pongor, S.
Trends Biochem. Sci. 1998 vol. 23 (9), pg. 341-346. PMID: 9787640
More references for model.it are listed here.
PyMOL is described here.
Clarifying Software Attribution: I, Wayne, am not involved in the model.it or PyMOL software at all. Those listed above are the developers and distributors of model.it. See their materials. See the PyMOL site for information on that. I simply set up this repository to make the software useable without installation headaches in a reproducible manner that can scale .
If you are just trying to get the PDB files for models few sequences, go to the the model.it Server.
This repository is set up to allow automated prcoessing of sequences through the model.it server with additional visualization by PyMOL. Start by pressing the launch model.it
button above or below.
In the notebook launches, I have added some examples illustrating how to use the pipeline. You can also add your own data and run it through.
The PyMOL images can be colored to reflect curvature and bendability if bendIt data is provided from results run through the bendit-binder pipeline.
This repository is set up to make use of the binder service offered by MyBinder.org. See their site for more information about Binder.