pendolino

generate_chromosome.py Arguments:

-n number of parts of chromosome (default = 1000)
-r required average distance of a part from the center (default = 5.1)
-m prefix of the names of generated files
-d delta (the larger, the less likely to make distance-incresing moves) (default = 3)

The script creates three files:

The script prints some self-explanatory information during the process.

position_the_chromosomes.py Arguments:

The script creates multiple files:

final_chain_i.pdb - decondensed i-th chromosome-chain
positioned_chain_i.pdb - positioned condensed i-th chromosome-chain
lamin_laminfin.pdb - lamin
chain_i_step_k.pdb - i-th chromosome-chain after k steps of decondesation (after every 10 million steps)
final_chains - python-pickled chromosomes-chain data after decondensation

The script prints the progress (current step [out of n steps]).

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
README.md		README.md
final_chain_1.pdb		final_chain_1.pdb
final_chain_2.pdb		final_chain_2.pdb
final_chain_3.pdb		final_chain_3.pdb
final_chain_4.pdb		final_chain_4.pdb
final_chain_5.pdb		final_chain_5.pdb
final_chain_6.pdb		final_chain_6.pdb
generate_chromosome.py		generate_chromosome.py
lamin_laminfin.pdb		lamin_laminfin.pdb
pendolino.py		pendolino.py
position_the_chromosomes.py		position_the_chromosomes.py
positioned_chain_1.pdb		positioned_chain_1.pdb
positioned_chain_2.pdb		positioned_chain_2.pdb
positioned_chain_3.pdb		positioned_chain_3.pdb
positioned_chain_4.pdb		positioned_chain_4.pdb
positioned_chain_5.pdb		positioned_chain_5.pdb
positioned_chain_6.pdb		positioned_chain_6.pdb

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