August 2026 - ChimeraX-users - RBVI Mailing Lists

halfbond false
by Timothy Springer 23 Aug '26

23 Aug '26

I want to set halfbond false for a pseudobond in #1.1/B what is exact command? - Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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Re: Using ChimeraX for private research
by Tony Schaefer 21 Aug '26

21 Aug '26

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(a)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(a)gmail.com> > *Sent:* Friday, 21 August 2026 08:32:47 > *To:* Adrian Tudini <ecovib2d(a)live.com> > *Cc:* Tom Goddard <goddard(a)sonic.net>; ChimeraX Users Help < > chimerax-users(a)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(a)cgl.ucsf.edu> wrote: > > Thanks > > Get Outlook for Android <https://aka.ms/AAb9ysg> > ------------------------------ > *From:* Tom Goddard <goddard(a)sonic.net> > *Sent:* Friday, 21 August 2026 08:15:46 > *To:* Adrian Tudini <ecovib2d(a)live.com> > *Cc:* chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)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(a)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. > > > > <image.png> > > > Adrian Tudini > Sole Trader > ECOVIB2D > Email: ecovib2d(a)live.com > website: https://ecovib2d.com.au/index.php > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: > https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: > https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > >

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Using ChimeraX for private research
by Adrian Tudini 20 Aug '26

20 Aug '26

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. [cid:c82064af-0038-4520-871e-6621d9342700] Adrian Tudini Sole Trader ECOVIB2D Email: ecovib2d(a)live.com website: https://ecovib2d.com.au/index.php

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Using Blotz in ChimeraX 1.12 issue
by Ferguson, Connor 19 Aug '26

19 Aug '26

Hello, I am attempting to examine the interaction of a viral RdRp with single stranded RNA. I downloaded Blotz as prompted, but it ran into an error downloading. I deleted the folder and redownloaded it with seemingly no issue. However, When I put in the RNA alone in an attempt to also get the secondary structure of the ssRNA, or when I put both the RNA and the predicted protein structure, I get the error message "Your Boltz installation does not have a molecular structure for PDB chemical component dictionary code ALA either because that code is new or is mistyped. You can try specifying that ligand using a SMILES string from https://www.rcsb.org/ligand/ALA instead of using its CCD code." I do not know why this message is occurring because even with the RNA alone this occurs (which the RNA should not care about alanine?). Any assistance or guidance on this matter would be greatly appreciated. Connor Ferguson Graduate Student, Virology Lab Teaching Assistant Department of Biological Sciences The University of Tulsa 800 South Tucker Drive Tulsa, OK 74104

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Change default molecule display to cartoon only (hide atoms)
by ramy.kazan＠ibpc.fr 18 Aug '26

18 Aug '26

Hi all, When I open a large model (e.g., a ribosome) in ChimeraX, the default display style shows it as atoms in the spheres style. I’d like to change this so that, by default, all atoms are hidden, and the model is displayed as a cartoon only. I’ve created an alias with the necessary commands and mapped it to a function key for quick adjustments. However, this approach has a limitation: after customizing one model (e.g., showing specific residues as atoms), opening a new model and using the function key overwrites the customized residues, applying the "cartoon-only" style to all open models. There must be a setting to adjust this behavior, but I haven’t been able to find it. I also recall reading that ChimeraX treats small and large models differently—perhaps based on the number of chains or residues—but I can’t remember the exact rules. Could someone point me to the correct way to set this as the default behavior for all new molecules? Thanks for your help! Best regards, Ramy

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PAE and ipTM scores
by Timothy Springer 18 Aug '26

18 Aug '26

The PAE viewer in Chimerax is wonderful. I can delete residues with low confidence pLLDT in the AF3 model (B factor <55) and the PAE viewer still works (only problem is deleting whole chains). Is there a way to delete the same residues and get revised pLLDT scores? I want them per interface in a multichain complex. - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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Regarding playing a series of volumes that are not a series
by Nour Mustafa 11 Aug '26

11 Aug '26

Dear All, I was wondering if there is a way to play a few volumes as a series when they are not in fact a series? I tried running 'vseries play' then listing the volumes individually, e.g. (vseries play #1,2,3) I tried grouping them and running vseries play again with the group's ID, but that also didn't work. Or is there a way to 'label' a group as a vseries so I can run that command, for example? I couldn't find a solution through my search. The volumes were initially a group, but I had to flip them on the z-axis and that broke the series and resulted in separate individual volumes. Sometimes I also want to compare volumes that are not a series by playing them. Thank you all in advance. Kind regards,

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clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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Feature request: expanded CORS options for remotecontrol
by Rich Waldo 07 Aug '26

07 Aug '26

Hello! Thank you for the work you do making structural biology possible! I was wondering if it would be possible to allow the remotecontrol rest start cors parameter to accept a list of allowed origins in addition to true (which I imagine would become an alias for http?://localhost:*,http?://127.0.0.1:*) or false. I have a browser extension I've written to make downloading volumes from CryoSPARC easier and I'd like to tell ChimeraX to first try opening the destination filename and only download the volume if that fails, but since my origin is not localhost I'm blocked by CORS and can't tell whether opening the volume succeeds or fails.

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Opening a PYMOL pse file
by James Prestegard 07 Aug '26

07 Aug '26

Is there a simple way to open a PYMOL pse file in chimera?

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