No no, by restart he just means close/quit Avogadro and then launch it again.
If you do that and it’s still not showing up in the menu, then something’s wrong. Could you maybe run Avogadro from a terminal and post all the stuff that gets written in the terminal when Avogadro is starting?
To be clear, what that means on a Mac:
/Applications/Avogadro2.app/Contents/MacOS/Avogadro2We want the text to see if it found the script and if it’s having some problem.
Hello matterhorn103 and ghutchis thank you for your kind informative and prompt update:).
Subsequent to following your instructions the attached within my Iterm was generated, feel free to update me accordingly towards a solution, thank you again:)
Iterm_Print_Out.txt (7.7 KB)
@mjsubach While unable to provide help to solve the problem, I recommend to revise and edit the log posted to facilitate reading. Consider one of the three options:
shell). See for instance the compilation by learnxinyminutes. As an example:``` shell
$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description: Debian GNU/Linux trixie/sid
Release: n/a
Codename: trixie
```
to yield
$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description: Debian GNU/Linux trixie/sid
Release: n/a
Codename: trixie
example.txt (142 Bytes)
example.txt.tar.gz (251 Bytes)
Hello Thomas thank you for your kind update:) and I amended my previous post deleting the log posted and adding instead a .txt file as recommended, thank you:)
Well maybe Geoff can give some insight as to why the script isn’t being dealt with correctly after the drag-and-drop but it looks like it’s not being put into the right place by Avogadro.
Try putting the file manually into one of these two paths:
"Checking for commands scripts in path /Users/joelsubach/Library/Application Support/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /Library/Application Support/OpenChemistry/Avogadro/commands"
Then it really should appear.
Hi matterhorn103 thank you for your kind update:).
I do not have either of these paths within my Mac, maybe this is whats causing the problem and or maybe I should create one of these paths, for example see screenshot where the Library subsequent folder does not exist after joelsubach, similarly after Application Support there is no OpenChemistry. Thanks if you know:)
I suspect it might be there, just hidden. It’s been a good 7-8 years since I used macOS regularly so I don’t know all that much about these things, but take a look at this and see if you can make /Users/joelsubach/Library visible.
By default, Apple hides your Library folder. It’s there, but hidden. (Beginner users might toss it and lose their preferences, etc.)
The easiest way to check it out in the Finder. Go to the “Go” menu and you’ll see near the bottom a “Go To Folder” command.
You can type in whatever path you want, and typing tab will help auto-complete.
This will let you go to whatever folder you want, even if it’s hidden. I suspect it’s used by Apple Tech Support and developers.
(I have no idea what “OpenMeta” is… I’ll investigate later.)
Hello matterhorn103 and ghutchis thank you for your kind and informative/prompt updates:)
Yes I accessed this privacy Library Folder within my Mac but as you can see from the screenshot attached that the Application Support extension is not exhibiting the OpenChemistry, accordingly suggestions? Thanks again:), Joel🚀
Well, that explains why it didn’t show up. I’ll have to check the code for drag-and-drop. Evidently it didn’t create directories if they didn’t exist.
While you’ve got that open, create the following nested directories:
OpenChemistry / Avogadro / commands
Then toss the Python script into commands and you should be good to go.
Thanks for helping us find the bug!
Hello ghutchis thank you for your kind update:).
I followed all of the instructions in this thread and loaded my ligand and executed Build → Invert Through Center → labeling the proper C inversion center atom along with checking copy, however, am not visually seeing the inversion on the Avogadro2 Screen nor have the coordinates beneath the Molecule left handed margin changed upon saving and visualizing them. Maybe it has something to do with activating Python appropriately i.e. Extensions → Download Plugins?, I dont know.
I believe that the procedure is simply the above with the new coordinates being generated beneath the Molecules Tab and visualized on the Screen at once correct? Thanks and your very welcome:)
Glad to hear that the plugin is finally loading and showing up! Sorry it took so long to get to this point.
As far as I know Geoff hasn’t checked out the script himself so best I answer your questions on actually using it.
Nope, if the command is showing up then the whole Python setup should be working properly.
The usage should be pretty simple. You know that only the atoms you have selected will be moved/copied right? So first use the Selection Tool to mark the atoms you want i.e. your existing water molecule. If nothing is selected (highlighted blue), then nothing will be done.
Then just choose Build → Invert Through Center, pick the atom you want as the centre, choose whether to move or copy, then click OK.
Hello Matterhorn103 and ghutchis thank you for your kind, informative and prompt updates).
See screenshot attached with the star representing the flipped water molecule, Beautiful!
(And for your enrichment the circled original water exhibits the interference precluding me towards the subsequent Opt Charges Tab within ffTK towards parameterization.)
I am unsure of the forum protocol, accordingly may I recommend this link to the VMD and Orca Forums where I had originally posted this inquiry without success if they accept? Best, Joel 
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