New user with two specific questions

General Discussion
1

Hi there: retired chemical engineer here with an ongoing interest in physical property correlations, which led me to find and download Avogadro (version 1.97.0, running on Windows 10, 64 bit). It seems fairly intuitive but I have a couple of getting-started questions:

  1. Like 99.9% of users, I can’t draw with pinpoint accuracy, so a six membered ring (as an example) doesn’t come out looking like a regular hexagon (e.g., not all single C-C bonds look the same in length). Am I correct in assuming that Avogadro ignores that when calculating properties, and assigns correct bond lengths, etc. automatically?
  2. I’m interested in solvent accessible surface areas, among other things. I found that it’s possible to calculate that property for any drawn molecule, but I don’t see how to display the results. How do I do that, please?

Thanks.

1 Like
2

Glad to know it’s helping!

It won’t assign correct bond lengths automatically because someone may want to run calculations with specific geometries (e.g., bond breaking, etc.)

Generally you’ll want to clean up the geometry. In Avogadro 1.97, try Extensions => Open Babel => Optimize Geometry or Control-Alt-O on Windows.

(There will be a more obvious “Optimize” function in 1.98 - it’s been a busy semester so far.)

In principal, it should be turning on the “meshes” display type automatically, but if not, it’s on the list of render types on the left panel.

3

Thanks. Now: how do I see the actual value in Ų of the solvent accessible surface area that’s been calculated? I see the representation using “meshes” but not a numerical result.

4

  • One approach useful if your computer is connected to the internet is to skip drawing altogether, and import structures of interest e.g., by their name (File → Download → Download by Name), e.g., cyclohexane. This resolver (possibly via NIH’ cactus server) equally accepts CAS registry numbers (50-99-7, or 492-62-6; both numbers refer to glucose).

  • A second, eventually independent of a working internet connection, is Avogadro’s collection of recurrent building blocks accessible via Building → Insert → Fragment. In the section of cyclic_alkanes, the then newly displayed widget offers e.g., cyclohexane.cml as well as specific conformations cyclohexane-boat.cml, cyclhexane-twist.cml, and cyclohexane-twisted-boat.cml for an import.

    To enjoy this, you have to extend once Avogadro via Extensions → Download Plugins → Molecules; this installation requires connection to the internet. Over time, you get familiar with the structures you use more often to attach an additional chain, substitute an atom, etc. It is a handy feature to save effort and time.

5

Nice to know. Thanks for the insight.

6

The default installation should include the molecules. The download feature just allows you to update as needed. (I don’t expect too many updates though.)

7

At the moment, it’s not available. I’ve got the code (e.g., add up the area / volume of the triangles) but need to throw in a dialog.

Hopefully I’ll have a chance to do that this weekend - at which point I’ll post a nightly build with the implementation.

8

Wonderful! I’ll be watching/waiting. Thanks very much.

9

Has that build with implementation of solvent accessible surface areas been posted, ready for download, please? Thanks.