1
$\begingroup$

I have this structure figure 1, I want to visualize by Avogadro, but the shape is not as I want like in figure 2 where I used Molden, so how can I make Avogadro draw the coordinate bonds.

Figure 1

figure 2

$\endgroup$
2
  • $\begingroup$ What Avogadro version? What format are working with (I hope it's not *.xyz)? Could you post the file content? Have you tried to manually connect atoms? And why organic-chemistry tag? $\endgroup$
    – andselisk
    Jul 9 at 11:58
  • $\begingroup$ Sorry for Tag organic chemistry the version is 1.2.0 it is not xyz file, it is different (file from CASPT2 Calculation) as I want to visualize the molecular orbital. $\endgroup$ Jul 9 at 12:01
4
$\begingroup$

The first representation is ball and stick, because atoms represented as spheres, and bonds in rod-like shape. The lower illustration is an example of stick, where atoms and bonds share the visualization as a stick. The question is not limited to the visualization of coordination compounds, nor the file type read by the program. If you use Avogadro 1.2.0 (e.g., from Linux Xubuntu 18.04 LTS)* then

  • go Settings -> Toolbars -> Tools to enable the relevant toolbar which show a button «Display settings»

  • a click on this button opens a new GUI. Here deselect the entry «Ball and Stick», and select instead «Stick». With default parameters (via the small wrench symbol at the right hand side you may adjust them), having both options enabled will yield an image like using «Ball and Stick» only.

enter image description here

*) You may be interested to join the Avogadro discourse to stay informed about recent developments of the program (e.g., announced release 1.9.4 a few days ago, entering debichem; or a glimpse about an improved Avogadro2 anticipated for fall 2021 here).

$\endgroup$
2
  • $\begingroup$ Thank you for your answer, I still have the same problem but ok, I will complete working with molden or gmolden. $\endgroup$ Jul 9 at 15:18
  • $\begingroup$ For files types anticipated to be read, Jmol has lists (example) and test files (repository). I don't know CASPT2 you mentioned, nor if there a similar public repository of a test output (atom location + orbital's information). $\endgroup$
    – Buttonwood
    Jul 9 at 16:29

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.