Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai