Software recommendations for Drawing Molecules

AI Thread Summary
For digital molecule drawing, users seek software that allows for both space-filling models and 2D representations of molecular structures. While programs like GeoGebra offer some drawing capabilities, they are primarily mathematical tools rather than specialized chemistry software. ChemSketch is frequently recommended for its user-friendly interface and biochemical pathway capabilities, and it is free to use. Other notable software includes ChemDraw, which provides 3D model output but requires a paid license, and Avogadro, known for its ease of use in drawing molecules. Online tools like MolView and PubChem are also mentioned for their accessibility and functionality. Users express a desire for programs that can integrate with chemical databases for quick access to molecular structures. The discussion highlights the importance of having both 2D and 3D visualization options for effective molecular representation.
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What do people use for drawing molecules (in a digital manner)?

I would like to make space filling type models as well as letters representing the atoms connected by lines at different angles.
The second kind I could make with ad drawing program, but there's got to be a better way.
 
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Geogebra maybe? If you want post a hand-drawn sketch, and I'll send you back the Geogebra file. Is it a 3D drawing?
 
mcastillo356 said:
Geogebra maybe?
Thanks for the suggestion. :smile:

Checked it out quickly on line.
Looks like a math program with some drawing capabilities rather then a chemical drawing program.
I am getting old and lazy and just want a simple molecule drawing program.

Probably also, connected to some data base of chemicals, so you could say ethanol and it would bring up the structure.

The drawing of the two different kinds of diagrams could be done by different programs.
Although both together would optimal.

mcastillo356 said:
Is it a 3D drawing?
I would be using 2D drawings as the output, but the space filling ball models come in 3D (as I understand) and you then get a 2D rendering of that.
Being able to rotate the molecule vs. view before rendering would be useful in making figures.
 
I like GeoGebra.
Glowscript/VPython (at Glowscript.org or trinket.io) is another possibility.
However, those are more general purpose... not really Chemically oriented.

These might be useful:
https://molview.org/
http://biomodel.uah.es/en/DIY/JSME/draw.en.htm
https://pubchem.ncbi.nlm.nih.gov//edit3/index.html
https://chemagic.org/molecules/amini.html

If any of these latter ones output your creation in a standard format,
one could view the structure in another viewer, like the ones at the top or some other 3d viewing program.
 
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Chemsketch was always my first choice.
 
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ChemSketch gets another recommendation from my friendly neighbourhood chemist (Mrs. Ibix). It's free, which is a bonus.
 
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I use ChemDraw package which includes 3D model output of the input chemical structure. It's not free though. I use my university license.
 
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What about programs that could draw whole biochemical pathways?

Anybody know any thing about programs that do that?
 
  • #10
BillTre said:
What do people use for drawing molecules (in a digital manner)?
Many years back, I attended a molecular modelling workshop, and we were taught how to use Avogadro. It's open-source. I stopped using it since a long time because I moved over to particle physics, but as far as I remember, it was fairly easy to draw molecules using this software.
 
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Borek said:
Chemsketch was always my first choice.
BillTre said:
What about programs that could draw whole biochemical pathways?
I'm not sure if this is what you mean, but looking though the ChemSketch pages, it does include some biochemical process capabilities:

https://www.acdlabs.com/download/quickstart/draw/QSG_ChemSketch_BiosequenceTools.pdf
 
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berkeman said:
I'm not sure if this is what you mean, but looking though the ChemSketch pages, it does include some biochemical process capabilities:

https://www.acdlabs.com/download/quickstart/draw/QSG_ChemSketch_BiosequenceTools.pdf

Looks interesting.
It looks like it requires some additional software to run on Macs.
I'll probably be getting a new Mac soon (see below), so I'll have to determine if it will work on a new machine (with a new processor).

My old apple laptop now has hardware problems.
I have just figured out that my battery is swelling up (a known problem).
It is recommended to get battery replaced, but I'll probably get a new 13" M1 macbook pro (I want a larger screen but those versions have not come out yet).
Then I'll probably get the battery fixed afterwards and figure out what to do with the old machine (recycle to a relative or trade in for new computer for relative).

I'll have to deal with the hardware first.
 
  • #13
BillTre said:
I have just figured out that my battery is swelling up (a known problem).
They should call it MacGout. 😂
 
  • #14
You might try an online application.

MolView

Kind of easy to use.
 
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@BillTre yeah the reactions of each of over 70 enzymes well-charted ##\dots##
 
  • #17
sysprog said:
@BillTre yeah the reaction of each of over 70 enzymes well-charted ##\dots##

I have an old book that has similar figures.
I like these overviews of the processes.
Metabolism is impressively complex.
 
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