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I am new to Blender, so this is probably a common question.

The origin and the 3D axis indicator are in different locations. This affects how modifications applied in edit mode via S and mouse drag.

I found the N panel that lets me enter origin location. How do I set the location of the 3D axis indicator?

Also, how is there any way to lock the origin so that it does not change with every left mouse click?

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    $\begingroup$ You're mixing several terms. Position of the axis indicator (it would help if you show screenshots btw) is called the pivot point; it will be the same as 3d cursor if pivot is 3d cursor. Origin of the object can't be moved neither with left nor right click, it's only Move Origin command or moving geometry in Edit mode. Precise location of the 3d cursor can be set in N panel as well in 3D Cursor rollout. $\endgroup$ – Mr Zak Jun 10 '17 at 15:30
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The 3D-Cursor is one of the unique and very useful features of Blender, albeit sometimes confusing to new Blender users.

The issue you mentioned seems to be because of the pivot center for rotation and scaling set to use the 3D cursor PERIOD key (the before the ? key).

If you press COMMA key the rotation/scaling transformations occur about the Bounding box of the current selection.

The 3D cursor has many uses in Blender.

  • The 3D cursor is where new objects get added in the scene
  • The 3D cursor can also be used for setting a temporary pivot axis for an object and then perform rotations and scaling (by pressing PERIOD). To reset the 3D cursor back to world origin, press SHIFT + C

Custom 3D Cursor placement behavior

If you really do not want the 3D cursor to be shifting when LMB is clicked, then you can customize it from the user preferences. This is an advanced customization step and must be followed carefully.

  1. Invoke the User Preferences Window CTRL + ALT + U
  2. Search for Set 3D Cursor
  3. Click the white triangle to expand the key map.
  4. If I want the 3D cursor to be placed when I hold SHIFT and CTRL keys and then press the left mouse button, so I check SHIFT and CTRL.
  5. Try it out in 3D view
  6. If satisfied, save the user preferences.

enter image description here

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That's not the origin, it's the 3D cursor. Not wanting to move it, is akin to trying to work with a text editor without moving its cursor.

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  • $\begingroup$ I am looking at an example where the 3D axis indicator (the 3 arrows showing x,y,z) is different than the origin. The origin (the dashed circle) is in the center of a cylinder. The 3D axis is affixed to one of the ends of the cylinder (different for the origin). I would like to move the axis indicator to the cylinder end. I see how to move an origin. How do I set the location of the axis indicator? Secondly, the origin changes every time I left click. Is there a way to lock this during edits so that I don't have to reset it all the time? $\endgroup$ – Doug Kimzey Jun 10 '17 at 14:48
  • $\begingroup$ Every object has an origin (its "position" in the world), The world also has an origin at (0, 0, 0). The red/white dashed circle is not an "origin", it's the 3D cursor. You can configure Blender to use it as pivot point for certain operations -- Blender can use the 3D cursor, object origins, the average point of all selected objects' origins, etc. Please see the 3D cursor and Pivot point manual sections. $\endgroup$ – dr. Sybren Jun 12 '17 at 10:11
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Pressing Shift+C will return the cursor to the center of the xyz axis (and re-center the scene visually if there are objects in it).

Pressing Shift+S reveals a drop down menu with many useful options.

shift + S menu

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