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
valence and geometry to sensible values based on the atom environment.
For example, if you construct aniline using the builder the nitrogen has
geometry=3 and valence=3. If you try to convert it to a sp3-hybridized
nitrogen via "replace N, 4, 3" it keeps geometry=3 and valence=3. You
can query the geometry and valence by selecting one or several atoms and
use the command:
cmd.iterate("sele", "print(name, geom, valence)").
Next you convert the N-conjugated "double bond" of the aromatic system
to a single bond using the builder. The nitrogen stays planar and the
geometry ist still 3. Now the command "replace N, 4, 3" works as the
nitrogen is no longer next to an aromatic system.
Best wishes,
Norbert
Am 06.02.2025 um 17:54 schrieb Lei Qian:
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>replace N, 4, 3
PyMOL>replace C, 4, 4
I tried to replace the atom in different types of bonds:
single/double/triple bonds, but the geometry value is always 4.
Could you please help me figure it out? Thank you very much!
Best,
Lei
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