If we want to visualize Z-matrix style molecule in tools like PyMol, we have to convert it into 'xyz' format first. is there any tool/software that can directly visualize Z-matrix format? Anything that is free and supported in Linux? Web tools are also welcome. Thank you.
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- 2$\begingroup$ +1. Any software that provides you a visualization of a molecule using only the Z-matrix, will most likely be converting the positions of the nuclei into Cartesian coordinates internally, since this is usually how "plotting" works: a set of (x,y,z) coordinates are provided and plotted. I understand that you are more interested in being able to plot a molecule that is represented in Z-matrix format without doing this conversion yourself, but this conversion will probably at least happen internally no matter what. Related: reddit.com/r/comp_chem/comments/xlajdz/zmatrix_viewer. $\endgroup$Nike Dattani– Nike Dattani2025-08-15 11:59:48 +00:00Commented Aug 15 at 11:59
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Avogadro can do this. It is a free software that can write and read z-matrix files. Copied directly from the linked website
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
You will have to write the input file in the z-matrix format, and then save it with the .gzmat extension. Now, if you open the file in Avogadro, you will be able to visualize the file. However, I agree with the comment by @NikeDattani that the conversation from z-matrix to Cartesian coordinates will happen internally.
This is the z-matrix file for water
%NProcShared=2 # opt freq b3lyp/6-31g(d) Water 0 1 O H 1 0.99025 H 1 0.99025 2 104.51000 You can save this as water.gzmat and open it back in Avogadro to visualize the structure.
