A more hands-on way of visualizing macromolecular molecules, is by 3D-printing. Companies like shapeways.com have long offered easy and relative affordable access to 3D prining of molecular molecules based on PDB files. However the affordable part only holds true for relative small 3D models and there is also an upper limit to the max dimensions they can print your model in.
This is probably common knowledge for many crystallographers using Coot, but I had never customized Coot before, so I had to figure out how to do it.
Turns out it is pretty simple (at least for the linux version that I use) and you can basically change whatever you want to. There are multiple ways, but I find it easiest to use the ~/.coot file. NB. Coot does not create the ~/.coot file but will read during startup it if it exists.
I was recently part of a project that got a publication accepted in PNAS and therefor I decided to try and make a cover design just for fun, but with the hopes that the editor would put it on the cover
Anyway the final design ended up like his:
At the homepage for Garib Murshudov’s lab, there is a page dedicated to EM fitting tools and scripts. Among these scripts are some for Coot which adds jiggle-fit, morph modeling and user-define restraints capabilities to Coot (you can read a bit about them here).
If you have not used Jiggle-fit yet, I can highly recommend it, especially for low resolution de-novo building.
Here is an example I did using jiggle-fit in Coot using my own map and a Coot generated ideal RNA double helix. Continue reading The power of jiggle fit in low resolution data