Vintage map maker

From a .mrc map, create a virtual vintage-style representation or templates for a physical version. Tested on MacOS, but should work on Linux also (perhaps with minor tweaks).

Virtual vintage-style maps

1. Install the necessary packages. This assumes you have virtualenv installed.

./setup.bash

2. Edit the map generation parameters. You can run the script from command line, but I found it easier to use the script virtual_runner.bash.

See the parameters using

python3 vintage_map_virtual.py -h

Edit the virtual_runner.bash as you see fit.

Note: Resampling the map takes time and the data requirements grow as the cube of the factor provided. I typically use 1-2 for testing, and 4-5 for the final run.

3. Run the virtual map maker. After editing the virtual_runner.bash script, run it using

./virtual_runner.bash

4. Chimera rendering The virtual_runner.bash should automatically launch Chimera. You will need to then open the chimera_script.py, which should then re-draw the maps in a vintage style.

Physical templates

1. Install the necessary packages. This assumes you have virtualenv installed.

./setup.bash

2. Edit the map generation parameters. See the parameters using

python3 physical_map_virtual.py -h

Edit the physical_runner.bash as you see fit.

Note1: I would suggest using the virtual map maker to optimize everything before creating a physical template.

Note2: The critical parameter here is the physical slice thickness. This then determines all other real-world dimensions.

Note3: Resampling the map takes time and the data requirements grow as the cube of the factor provided. I typically use 1-2 for testing, and 4-5 for the final run.

Note4: While the pdf maker '''should''' render on the proper page size, I noticed the printer did its own rescaling. Therefore, for practicallity I used the slice images and manually rescaled them in MS Word to print at the proper size.

3. Run the physical map maker. After editing the physical_runner.bash script, run it using

./physical_runner.bash