Hi Helge, That is a bug. Placing a marker in a map with the mouse should put it where you clicked the mouse even when the marker set has been moved relative to the map. I will fix it in tonight's ChimeraX daily build. Thanks for reporting the problem. Tom

On Mar 9, 2021, at 2:08 PM, Helge Paternoga <Helge.Paternoga@chemie.uni-hamburg.de> wrote:

Dear ChimeraX team,

I have a question regarding the placement of markers.

I am currently trying to extract densities from cryo-EM maps for figure preparation. Therefore, I am using markers to colour any density that is not part of what I want to extract and then split the map accordingly.

I noticed that when I translate a markerset, e. g. by using "view position" with "sameAsModels", new markers are not placed at the cursor position, but instead are transformed according to the translation of the whole markerset. Therefore, to move markers, I have to use the "move marker" command on each marker separately. I would like to know if this behaviour is intented and if it can be switched somehow to place markers at the cursorposition even after translation of the markerset.

Ultimately, I would like to re-use defined markersets for extracting (or "cleaning") the same invariant components of my maps. But the current behaviour makes it nearly impossible to add new markers for touch-ups after opening and aligning a markerset.

Best,

Helge

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