If you want to visualise your chemical crosslinking-mass spectrometry (XL-MS) data on protein structures or structural models in PyMOL, try our new plug-in! PyXlinkViewer automates the display of crosslinks on a 3D structure, and calculates Euclidean distances between crosslinked residue pairs. It also allows you to control the types of crosslinks displayed (interprotein, intraprotein and dead-end) and edit their display properties.
Our paper describing PyXlinkViewer has just been accepted in Protein Science and you can download the plug-in from GitHub. If you have any feedback, or need help using PyXlinkViewer, feel free to get in touch.