Hi Sean, Unfortunately this is a limitation of the fly command in ChimeraX -- it is not interpolating clip planes. This should be in the fly command documentation -- we will add it. I figured it out by looking at the Python source code for fly where a comment says "TODO: Handle clip planes" https://github.com/RBVI/ChimeraX/blob/4f602d03b911841d60db4826ce4140fd8fb0ae... Clip planes are interpolated when using the view command smoothly transition to a named view. So you can do view position1 20 view position2 20 ... and it will interpolate the clip planes. If you wanted to record a movie you would put these in a script and put "wait 20" after each view command so it renders 20 frames before going to the next frame. By the way, the ChimeraX resfit command does not use clip planes. It instead masks the map and shows only the nearby residues. You can see what it is doing in the Python source code here https://github.com/RBVI/ChimeraX/blob/4f602d03b911841d60db4826ce4140fd8fb0ae... All of these Python source code files are in your ChimeraX distribution so you can study them and modify them if you want to test new ideas. Tom

On Nov 3, 2023, at 7:43 AM, Sean Connell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello, I have a question about the fly command. I am trying to iterate over a series of saved views (p1-p6) using the fly command. The views are close-up views of residues because I am trying to make a movie similar to that made with resfit. The issue is that the cutting plans don't seem to update as it moves from view to view. Do you have a hint that could let me know what I am doing wrong?

Thanks for any tips you have

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