There are many ways to open a file in Avogadro. You can simply drag and drop it or even build with the SMILES. See the attached videos.

Hello,

This was an issue some years ago. You can check some old post related that: https://sourceforge.net/p/avogadro/bugs/770/

basically the site (http://cactus.nci.nih.gov/chemical/structure ) from which Avogadro imports the structure has moved (apparently moved from http to https). In new version (v 1.2), this problem should not arise since they've resolved the issue.

However, there are alternative ways to do what you're probably trying to do even if Avogadro can't fetch the structure.

1. You can draw the molecule from scratch using Avogadros draw tool (F8)

2. You can go to Build> Insert> Fragments. You'll find a plenty of molecular fragments there, which you can edit yourself to construct the structure you desire.

There are other useful options are there under "Insert" . So, give those a try.

3. Search online for the respective molecule, and download the 3D structure file (e.g .mol., .pdb .xyz etc) which are compatible with Avogadro. Then open with Avogadro. There are many resources and many database. Some example sites (where you can fetch, create and download a 3D model),

http://molview.org/

http://www.chemspider.com/

https://pubchem.ncbi.nlm.nih.gov/

Uttam Pal, Turbasu Sengupta Thank you very much for sparing out time from your tight schedule to elaborate on how to maneuver this challenge. On the issue of installing Avogadro V.12, I've done that once again, and tried it yet it produced same result (nothing appeared on my screen). I've also watched all the .gif file you uploaded. I copied the SMILES of the molecule and inserted it via "Build" yet no image showed up. Maybe I should give up on Avogadro. I actually have chemdraw, and GaussView and their know-how, although I wished to add Avogadro to my archive of tools. Nonetheless, thanks once again.

Before you just give up, I just want to ask, are you been able to visualize anything at all (molecule/atom) on the GUI window by any means? You can perform a small test. Just open Avogadro> Click on the Draw tool on the top if it is not selected already (The small pencil icon or keyboard shortcut F8). Now if you just make a left click on the GUI draw window it should build a methane molecule (attached screenshot). If you are not able to see even the methane molecule, then probably something is wrong with your Graphics Driver or Something related to that. Also, how about post some screenshots? What Platform are you on, Linux or Windows??

A question (May be a stupid thing to ask) just came to my mind, is the option 'Ball and Stick' (or alternative ''Stick' option) on the left window is ticked on? Otherwise you'll not able to see any Ball and stick model.

There was a display problem with some version of Avogadro with some version of Ubuntu (17.04 to be precise). Here's the bug report that I submitted then (https://github.com/cryos/avogadro/issues/865). It got fixed in Ubuntu 17.10. Which OS you are using? Maybe try it on a different machine.

Turbasu Sengupta Thanks for your kind assistance. Sure, I can draw structures with it, no doubt but the issue was about importing molecules and fortunately while typing this message, I did a run check once again, I can't tell what I click but the problem has been resolved now. Uttam Pal I use Window 10. Many thanks to you.

I can not recommend this software for serious work, the program is full of possibilities, I agree, but it is completely unreliable. At any time, it may stop opening files, or save them with errors. In the middle of the "optimization" critical errors can occur, and it does not matter how powerful the equipment you have.

The only advantage of it - for free.