Frequently asked questions

I am on Mac OS X; I updated to Mojave and I can't install the dependencies using brew. Help?

There have been some problems experienced after updating to Mojave regarding unusual permissions complaints from Brew. Reinstalling brew appears to solve this problem.

A second problem appears to be a failure of brew to to link the fftw library due to incorrect ownerships of files in the /usr/local directory. To fix this, re-exert your ownership over the files by issuing the command:

sudo chown -R $(whoami) /usr/local

and then attempt to relink again:

brew link fftw

I am on another Linux flavour and I am having generic trouble installing Vagabond. Help?

There appear to be at least two three I know can be encountered with installing Vagabond on CentOS and other systems.

Firstly: ninja does not want to install from the package manager. In this case, you can download it from

Secondly, the default flags for the C++ compiler does not include the c++11 standard library. To get round this, supply the additional command to meson. (You may need to delete your first attempt at build/current first.)

CXXFLAGS='-std=c++11' meson --buildtype=release build/current

Thirdly, the mouse events with Qt5 appear to come in a separate package on some systems. If you're getting compile errors due to a missing header file like this:

../../libgui/qtgui/VagabondGLWidget.h:15:35: fatal error:
Qt3DInput/qmouseevent.h: No such file or directory
#include <Qt3DInput/qmouseevent.h>

On CentOS, you may need to ask yum for another package qt5-qt3d-devel. On Ubuntu with apt-get you may want qt3d5-dev.

I am putting the average_X.pdb files back into other atomistic refinement programs and getting nonsense R factors. Why?

The average PDB files are good for loading into Coot for viewing the average position and derived anisotropic B factor equivalents, but these have not been generated from a Gaussian model and atomistic refinement schemes will interpret them as such. This means they don't translate well back to atomic coordinates and B factors. Therefore they are only good for viewing a summary of the ensemble. If you would like to change the model based on the electron density and refine with another program, change the original model (e.g. in Coot) based on the electron density calculated from Vagabond. It's safe, because the free reflections have been excluded from the map.