Can I superimpose a trajectory on an external structure, and if so, how?

In Suite 2012, you can place a structure in the Workspace, and superimpose the trajectory frames onto this structure. The superposition is done in the same way as in the Superposition panel with an ASL expression. This means that the atom ordering in the external structure must match the atom ordering in the trajectory, otherwise the results may be unexpected. If the heavy atoms are in the same order but the hydrogens are not, you could use an ASL expresssion that did not include hydrogens.

If the atom ordering in the external structure does not match the trajectory structures sufficiently well, you can consider aligning the external structure to a particular frame in the trajectory, and then superimposing to the trajectory frame.

Keywords: Desmond, Maestro

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