Home   Manual

Fetch by chemical name

I have a new installation of version 1.2 on a Mac and cannot get this key feature to work.
No matter what I type in the return is “specified molecule could not be loaded: name.sdf”
Any help hugely welcome

If you enter the folder containing your .sdf in question from the console (by cd or/and cd ..), are you able to get some visualization of the model e.g., by OpenBabel with either of the two following commands?

obabel -isdf input_file.sdf -O output.png
obabel -isdf input_file.sdf -O output.svg

This aims to check if the .sdf to be read is in good shape, and (still) may be read.

Hi Many thanks. I dont think this is a rendering issue. I “think” avagadro should be able to search for and import these files shouldn’t it? They are not local files

The NIH Chemical Resolver service, used by “fetch by name” changed their URL (i.e., requiring HTTPS).

So no, you can’t use this feature any more, and for technical reasons, we cannot easily produce more 1.2 releases.

It’s less convenient, but you can access this yourself, e.g.

Or, upgrade to 1.95, for example.

Hi Many thanks. Upgrade to 1.95?

I just tried in a more recent version 1.95.1 in Linux Debian 12/bookworm (branch testing), while being connected to the internet. File → Import → Download by Name, e.g., for keywords like water, benzoic acid, glucose, purin, glutamine. After confirmation (ENTER), briefly I see a progress bar. After that, I have to put the mouse on the canvas and click again with the left mouse button. For a new molecule, Del key clears the canvas.

However, there are keywords/names which this function does not successfully resolve yet (i.e., progress bar reaches 100%, disappears; click doesn’t let the molecule appear). Examples of unresolved names are acetone, thiophenol, thiophene, furan (though both THF and tetrahydrofuran work), benzathiazole, naphthalene.