Hi André,
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