Script for easily extracting the view matrix in VMD

I have been using VMD increasingly more since I discovered how powerful the included tachyon engines are in VMD for rendering. But since I started learning VMD I have been struggling with copying my work flow from PyMol to VMD. Especially my old routine where I always made pml scripts for all movie and images I made with PyMol, has been hard to transfer to VMD.

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Download Cryo-EM data via EMPIAR through FTP

If you need some Cryo-EM data to play with or for testing some new software etc. then an easy way to obtain either micrographs and/or particles is from EMPIAR. However if you wanna do it much less hassle-free than using going through the web interface, you can use FTP to download large amount of data from their server.

Below I have made a small example scenario from an Ubuntu terminal, that shows how I would normally do this, using EMPIAR entry 10028 as an example .

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Tachyon Ray-tracing

Recently I have been playing around with VMD and the included Tachyon ray trace engine. Once you get used to the weird selection algebra in VMD and accustomed to tcl scripting, it is truly incredible easy to use the Tachyon engine to  generates publication grade renders.

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I have been playing around with a LEGO program called Lego Digital Designer (LDD), where you can create your own LEGO creations etc.

Inspired by an older LEGO Ideas entry I wanted to reproduce the Tecnai Spirit G2 TEM I use at work, in LEGO.  Unfortunately

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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.

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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: 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:

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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.

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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 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.

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How to customize 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.

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An amateurish molecular visualization blog