Hi Reza, Using the volume path tracer tool (menu Tools / Volumes / Volume Path Tracer) you can place marker spheres (actually atoms) with the mouse and link them with cylinders (actually bonds). It is intended for placing markers on high density regions of volume data. But you can use it without any volume data if you turn on the "Drop markers on empbyt space with mouse" option. Also you can move markers if you click on the "Move markers with mouse" option in the volume path tracer dialog. The spheres and cylinders can have whatever radii and colors you like. The detailed documentation for this tools is in the Tools section of the Chimera User's Guide under Volume Path Tracer: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/vo... You can show this documentation in a web browser by pressing the Help button on the volume path tracer dialog. Tom