Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations
This notebook explain how to create an initial configuration for the Yeast nucleus, how to set a persistence length and how to run the simulation. The simulations will generate a trajectory file and also dumps the contact to compute hic matrices
In the following we detail all the other possibilities of this library
Library to create polymer path with given functionnality, such as some constrain on the position of any monomer. It is also possible to create polymer with some rigidity
What can be achieved with it:
https://www.youtube.com/watch?v=iwep58wIsuU
The easiest way: sudo pip install cpolymer
Here I show how to use the module to creato a block copolymer system:
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/cpolymer_demo.ipynb
Here How to create a polymer whose path has some specific constrain
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/polymer_path.ipynb
Finally a little bit of fun with the creation of a polymeric eiffel tower
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/cpolymer_eiffel_demo.ipynb
How to create a simple nucleus
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/Simple-nucleus.ipynb
How to create a Yeast nucleus
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/Yeast-Nucleus.ipynb
How to create a Yeast nucleus with a persistence length and dumping hic
How to create a Yeast and make it replicate!
http://nbviewer.ipython.org/github/jeammimi/cpolymer/blob/master/notebook/Cell_division.ipynb
Here is the video from the last notebook!
https://www.youtube.com/watch?v=iwep58wIsuU
First install vmd then use the script visu/rep.tcl : for example:
vmd -e ../visu/rep.tcl ./nucleus_yeastnoyau2.pdb dump_init.nucleus_yeast.comp.dcd final.xyz