Hi André,
On Feb 16, 2023, at 2:50 PM, André Graça via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone!
Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps?
No, though we have a feature-request ticket open in our bug-tracking database for this. I have added you to the recipient list for that ticket.
I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models?
Assuming those models are the only structures open, the below would save the distances to a file named "distances.txt" in your home directory: from chimera.atomic import all_atomic_structures s1, s2 = all_atomic_structures(session) from chimera.geometry import distance import os.path with open(os.path.expanduser("~/distances.txt"), 'w') as f: for a1, a2 in zip(s1.atoms, s2.atoms): print(a1, a2, distance(a1, a2), file=f) You could put the above in a file with a '.py' suffix and open it in ChimeraX to run it. --Eric Eric Pettersen UCSF Computer Graphics Lab