Large scale 3D printing

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.

Continue reading Large scale 3D printing

How to customize Coot

coot

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.

Continue reading How to customize Coot

My first attempt of a cover design

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:

Continue reading My first attempt of a cover design

The power of jiggle fit in low resolution data

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

Converting cryo-EM map to mtz

As I have not been able to find basic newbee information anywhere regarding how to convert a Cryo-EM map to mtz, I will just note down what I did. I have no idea if it is the “correct”way or not, but it works.

Basically I just used the phenix program: phenix.map_to_structure_factors with my EM map (in mrc or ccp4 format, they are normally identical formats) as input together with a resolution constant (d_min) e.g.

phenix.map_to_structure_factors CrappyEMmap.mrc d_min=4.4

and out comes a mtz file for you.

Increasing grid points in your EM map

If you want to make your crappy EM map look better( with look being the operative word, as the quality of the map is unchanged) when using e.g. coot, you might want to consider increasing the grid spacing, that is the number of sampling divisions along any of the axis.  It is basically the same process you use in PyMol when generating figures with a very fine mesh density, there it is just called map double . Continue reading Increasing grid points in your EM map

Cryo-EM

cryo_em_progress

So I have ventured into the Cryo-EM field recently, as so many others have done as well. This means that this page will see a bunch of small updates with stuff related to Cryo-EM (primarily de-novo model building, and refinement etc.) and not so much on molecular visualization. Not that I updated this page every week/month any way, so no big changes.