Modelling of Mycoplasma genitalium
Repository covering the ccsb work on the mycoplasma genitalium modelling project based on the WC computational model.
Recipes and models are available on Mesoscope in the list of available example (Load->New Recipe->From Example->Mycoplasma Genitalium
The repository consist in the following folders :
- cellPACK_Data : the copy of the data folder that is used by cellPACKgpu to load and generate the final 3D models.
- lattices
- palettes
- proteins
- recipes
- README
- LatticeNucleoids : David Goodsell software to generate initial configuration of DNA and RNA for the model.
- fortran source
- input files
- README
- Models : Exampe of generated models with cellPACKgpu in different file formats. cif and bcif can be directly loaded in molstar
- Model at Beads resolution in pdb format (.pdb)
- Model at Atomic resolution in cif (.zip) and bcif format ( convertion done with molstar ). See one example using a bcif file in molstar. Switch the representation to spacefill and add a clipping plane.
- Model in cellpack binary format (.bin) can be loaded in cellPACKgpu, mesoscope and molstar.
- Lipids Membrane model in cif and bcif format, with and without holes. Theses models presents overlap between lipids.
- Bundle in zip format for mesoscope
- Example of molx filem can be directly drag and drop onto the molstar viewer. You can open the following premade molstar scene with membrane and without. If you have a powerfull workstation try to load the model with spacefill representation.
- Scripts : Python's script integrating data from the WC computational model and structural information for MG proteins (in input_files folder). It generates: csv table used to make recipe in mesoscope, csv table used to make lattice-based models of supercoiled mycoplasma nucleoids with LatticeNucleoids by David S. Goodsell
- cellPACKgpu binary release : standalone windows executable