Hi Isabel, Yes, CoordSets are the way to go. Assuming you want to extract these distances without necessarily playing through the trajectory/morph, the plan would be:
(1) Get the coordinate set IDs from the structure
(2) Loop through IDs to get coordinate sets
(3) For each set, compute the distance
If your structure was in a variable named 's' and the atoms you wanted to measure the distance between were 'a1' and 'a2' then the code would be:
a1_index = a1.coord_index
a2_index = a2.coord_index
from chimerax.geometry import distance
for cid in s.coordset_ids:
cs = s.coordset(cid)
d = distance(cs[a1_index], cs[a2_index])
do something with the 'd' you just computed
Glad to hear you are going to continue improving the already excellent XMAS bundle!
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Good morning,
I am a student intern at the Richard Scheltema Laboratory, and I am going to be continuing with the modification of the XMAS bundle submitted to ChimeraX recently.
Right now, we are trying to extend the bundle to be able to extract specific distances between specific amino acids for two different proteins but for a molecular dynamics simulation. Either by loading a trajectory coordinates + topology files or by using the “morph” command and then “coordset slider”.
So, the idea would be to extract the distances between the alpha carbons, of a set of pre-selected amino acids, in each frame of the simulation. Do you have any suggestions about any modules or methods that I should look into to extract this information in each frame? I saw there is a CooordSets class but I do not know if this would be the right way to go about it.
Kind regards,
Isabel de Moya Clark