Use Pymol to generate many snapshots of polymer configurations, emphasis on chromosomal images.
Python Pymol If you are ssh'ing you may need to have the ability to x forward.
As seen in example.py, the idea is to programatically do the following for many snapshots:
- Use polymerMole.mainDefs.r2bdb to turn a file of x,y,z coordinates into a .pdb file.
- Create a pml file that specifies viewing options with polymerMole.mainDefs.makepmlFile
- Run pymol and save the output to file
Run example.py to see example of how the code works. This example code puts the output into the floder where the data came from.
Change the path and snapshot number in baseNames to the file you would like to plot.
Change the plotting details after #Example1/2 to those that you would like.
Most likely you will want to added new options to the code in mainsDefs.r2pdb and mainDefs.makepmlFile to your likeing.
Have fun!