Adrian, SEQCROW doesn't have an equivalent to Avogadro's optimization with a molecular mechanics force field. ChimeraX has a `minimize` command that might be similar to what Avogadro does. I think Avogadro lets you choose between UFF and a couple other force fields. SEQCROW does add a mouse mode for bonding atoms where you click on one atom then the other to create a bond. You can switch to it on the More Right Mouse tab near the top of the ChimeraX window. You will need to restart ChimeraX after installing SEQCROW to see the tab. For building starting structures, there's a couple options that I typically use. SEQCROW adds a 2D Builder tool that lets you draw a sketch of the molecule, and optimize the initial structure using a semiempirical method. If your molecule isn't too big, the optimization should be pretty quick. ChimeraX's open command can also take IUPAC names and smiles (e.g. `open iupac:benzene smiles:CC`). And for setting up inputs, SEQCROW has the QM Input Generator tool. You can use this to build input files for ORCA, SQM, and a few other QM programs. SQM comes with ChimeraX, and it's what the 2D Builder uses to optimize the structures. If the program is installed on your computer, you can also submit the job from the tool. Best, Tony On Thu, Aug 20, 2026 at 5:16 PM Adrian Tudini <ecovib2d@live.com> wrote:
Hi Thanks for that. Avogadro2.0.0 has a capability to select, say , a carbon atom plus an oxygen atom to bond together to form carbon monoxide. You can draw the bond between them by hand and then find the Ground state coordinates (exported to many file formats as an input -especially ORCA) by going through an optimization process. Orca also requires the charge of the system and the spin multiplicity with other parameters.
I hope thar helps.
Get Outlook for Android <https://aka.ms/AAb9ysg> ------------------------------ *From:* Tony Schaefer <tony.schaefer.chem@gmail.com> *Sent:* Friday, 21 August 2026 08:32:47 *To:* Adrian Tudini <ecovib2d@live.com> *Cc:* Tom Goddard <goddard@sonic.net>; ChimeraX Users Help < chimerax-users@cgl.ucsf.edu> *Subject:* Re: [chimerax-users] Re: Using ChimeraX for private research
Adrian,
Cube files are handled by Chimerax's parser. Seqcrow can show orbitals from the orca plain text output (usually *.out) using its Orbital Viewer tool if the job was run with !printMOs printBasis or equivalent settings. In the External QM Utilities tool you can have it run orca_plot on your gbw files, which will often be faster if you know what orbitals you want to look at.
I didn't notice they added intensities for anharmonic frequencies to the newer version of orca. I can get those to show in the IR plots soon.
I'm not exactly sure what you mean for the selecting atoms to build and optimize systems. Can you expand on that a bit more?
Best,
Tony
On Thu, Aug 20, 2026, 4:53 PM Adrian Tudini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thanks
Get Outlook for Android <https://aka.ms/AAb9ysg> ------------------------------ *From:* Tom Goddard <goddard@sonic.net> *Sent:* Friday, 21 August 2026 08:15:46 *To:* Adrian Tudini <ecovib2d@live.com> *Cc:* chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> *Subject:* Re: [chimerax-users] Using ChimeraX for private research
Hi Adrian,
Have you tried the ChimeraX SEQCROW plugin (install with ChimeraX menu entry Tools / More Tools...)? It has capabilities to visualize ORCA results and setup ORCA runs. I don't know details of its capabilities. It was written by Tony Schaefer who sometimes reads this mailing list.
Tom
On Aug 20, 2026, at 1:37 PM, Adrian Tudini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi
My name is Adrian and I am currently using ChimeraX for private research. In my use of ChimeraX, may I suggest some improvements for ChimeraX. If yes, they are listed below:
1. Currently ChimeraX displays a *.cube file with just one molecular orbital in it from ORCA 6.1.1 (processed by orca_plot). It would be nice if Chimera X can display all Molecular Orbitals of a system at the one time. 2. Display overtone and combination bands of an IR spectrum, again from ORCA 6.1.1. 3. Able to select atoms (elements) to build complex systems, then optimizing that system to find the Ground State of that system. Then exporting the co-ordinates of that system into an input file for ORCA 6.1.1 and beyond.
Just a few thoughts.
Thanks.
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Adrian Tudini Sole Trader ECOVIB2D Email: ecovib2d@live.com website: https://ecovib2d.com.au/index.php _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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