Molecular Maya renders

I made these renders using Autodesk Maya2016 (edu license) and Molecular Maya from Clarafi.  I am still learning how to use the software, which is incredible powerful and versatile. I have made a ton of weird renders already and these are just a small subset of them.

Continue reading Molecular Maya renders

Cryo-EM: How to change box size and pixel size

Short info that could be of interest for people new in cryo-E.

From the command line in a linux terminal you can look up the box size of the map you just created in Chimera by using EMAN2:

e2iminfo.py map_you_want_to_know_BoxSize_off.mrc

You can then change the box size (in pixels) the map by using Relion from the command line.

For example if you want to change the box size of your map to 300x300x300 pixels from whatever it was before, you just type:

Continue reading Cryo-EM: How to change box size and pixel size

Cryo-EM: How to generate an initial reference map from pdb

When starting out in the field of cryo-EM it is often the small annoying problems that you waste a lot of time on. These problems are often very difficult to Google as the experienced Cryo-em scientist often take the solutions to them for granted.

One such problem I found difficult in the beginning was how to generate an initial reference map from a PDB model. As always there are more than one way of solving this problem, but what I have found to be the best approach for people new in the field, is using Chimera for it. Chimera have implemented a EMAN program called pdb2mrc and called it molmap. By going through Chimera instead of generating the map via pdb2mrc in a linux terminal, you get to visualize the map and the pdb file, which I think is general easier for people new to cryo-EM. That being said I think pdb2.mrc is better as it has more options and it is the one I use now.

Continue reading Cryo-EM: How to generate an initial reference map from pdb

More Coot scripts

Continuation from How to customize coot:

On this site there is a whole list of incredible useful scripts for Coot. I have selected some that I am especially fond of, as they make every day building in Coot much more effective (for me at least) as you can minimize the amount time that is wasted clicking through various menus etc. Should be noted that you can download all of the scripts from the site in one single file here NB I am not the author to any of these, you can contact the author on: olibclarke at gmail dot com.

Undo active

Undoes modification to active molecule (getting the mol id from the atom you are centered on).
Avoids having to manually change the undo molecule. Currently bound to “z”. Continue reading More Coot scripts

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

An amateurish molecular visualization blog