Dear Lei,
the best way to build a new molecule is via the builder in the GUI.
The commands "replace" or "attach" are not well documented. I could
reproduce your problem and I think PyMOL runs some kind of check routine
after you issue a replace or attach command and it will reset the atomic
Dear users,
Could I ask a question on geometry option in replace command?
I tried to use Build/Fragment/XXX to replace an atom to a new one, and pymol
GUI shows the corresponding replace command.
However, I found the geometry option always equals to 4.
For example,
PyMOL>replace O, 4, 2
PyMOL>repl
