QuteMol tutorial – how to make realistic looking figures in 1 min

Just a short introduction to what could have become the perfect tool for generating high quality realistic renderings of PDB files, QuteMol.

QuteMol is an open source program for high quality molecular visualizations of PDB files only. QuteMol mainly differentiates itself from PyMol by its use of real time ambient occlusion and a incredible intuitive user interface.

As a token of just how easy QuteMol actually is to use, I created the below GIF on my own desktop computer in about 1 min.

Rotational gif of 80S ribosome made with QuteMol

Despite the GIF is a bit too fast, and only in 512 resolution It is truly impressive for such a small open source program to be able to create such high quality rendered GIF so fast.

Basically you install the program like any other windows or Mac program as they have installers for both. You can also find a precompiled version in the Ubuntu repositories or the actual source code  to compile yourself. However I have not tried any of the two latter options myself, only the mac and windows versions.

To get going simply load a PDB file of your choice, I used my ribosome pdb file. To begin with, the PDB file will be displayed in space-fill mode and you will be presented with 15 preset option to chose from


 My favourites by far are the “realistics 1 & 2”, “Molecule of the month” and “mixed 1 & 2” settings. Especially the “realistic” preset modes live up to their names, as the renderings look like high resolution photos of actual 3D printed models.

S.E.M 2 preset mode
Molecule of the month preset mode
Mixed 2 preset mode
Realistic preset mode

While the initial space-fill mode is great, QuteMol also offers two additional representation modes called  “licorice” and “ball’n’sticks”. You find the different modes under the “Geometry” tab.


All the 15 preset modes on the preset tab, can also be applied to the three different representation modes.  By combining the realistic presets with the licorice mode, on especially large molecules like the 80S ribosome, you can get some beautiful renderings:

Licorice representation mode, using the realistic 2 preset mode

In the Customize tab you can tune various settings to your liking. The different preset modes simply put these setting at specific values each time they are applied.


I personally find no reason to change most of the settings much except maybe the background color, that is if you dont use the transparent setting when saving a picture.

To create either GIFs or lossless  PNG/JPEG’s all you have to do is hit the button which looks like a camera and then change the filetype to the specific type you want.


When you hit save another window will open asking about some exporting settings such as: resolution, antialiasing and transparent background (only PNG). When saving a GIF you get a large array of different options to customize your GIF a bit more .


But just as great and easy QuteMol may be just as annoying and rigid it is when you actually want optimize beyond the few options you have access to. For example you only have the choice to color “per chain” or “per atom”. If your PDB file has lets say 6 chains in it, you will not be able to assign the same color to two different chains. That is unless you change the chain IDs so the two chains you want to have the same color have the same chain IDs,  but you have to do that in another program or manually editing the PDB file. Further more there is no manual color assignment option in the program, you can only change the whole color schema at once. This means that if you want e.g. chain B to be blue, chain A to be yellow and C to be red, you have to cycle through the different color schema until you hit the specific combination of colors you want, if you ever hit that combo that is.  This is just stupid and frankly makes no sense as to why remove so essential options. The program, at least the windows version also has some major memory bugs and will often crash when rendering GIFs or been used for too long to make single pictures with. and there is no autosave or anything, so you lose the color schema you have clicked 23 times to find etc.  

The really bad news is that QuteMol has not been developed since june 2007, so there is basically zero chance that any of the bugs or the lack of basic features will ever be resolved. A real shame!

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2 thoughts on “QuteMol tutorial – how to make realistic looking figures in 1 min”

    1. Hi,

      Unfortunately no I dont know, but I think it is not possible.

      Because of that I only use it on Linux (Ubuntu) where it works fine.

      you can even just write: “sudo apt-get install qutemol” to get it. so it is very easy.


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