August 2026 - ChimeraX-users - RBVI Mailing Lists

Solvent accessible area
by jianghai.zhu＠nih.gov 28 Aug '26

28 Aug '26

Hi, I'm using ChimeraX to calculate the solvent-accessible surface area (SASA) of a large complex. The output SASA is 6.1455e+05. It seems ChimeraX only outputs 5 digits. Is there a way in ChimeraX to output more digits, say one or two digits after the decimal point? When calculating SASA or other areas, ChimeraX doesn't seem to compensate for hydrogens if there are no explicit hydrogen atoms in the pdb file. Is it better to use "addh" before "measure sasa"? As far as I can tell, ChimeraX doesn't optimize the orientation of riding hydrogens like other programs, such as phenix.reduce. Is that correct? Thanks! Jianghai

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error installing phenix-ui
by Kevin M Jude 28 Aug '26

28 Aug '26

Hi, I’m using ChimeraX 1.12 from sbgrid for macOS. I tried to install the phenixui from More Tools and got this error: Could not find a version that satisfies the requirement ChimeraX-OpenCommand~=1.16 (from chimerax-phenixui) (from versions: none) ERROR: No matching distribution found for ChimeraX-OpenCommand~=1.16 Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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ChimeraX website down?
by Alexis Rohou 26 Aug '26

26 Aug '26

Hello, I'm currently unable to access the download page (or any page in fact) for ChimeraX: https://www.cgl.ucsf.edu/chimerax/download.html Cheers, Alexis PS. I have bcc'ed a few of the team directly in case the mailing list is also down

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halfbond false
by Timothy Springer 26 Aug '26

26 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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Error when trying to add the PhenixUI plugin into ChimeraX 1.10.1 on RHEL 8.10
by Pickering Joshua (External) 26 Aug '26

26 Aug '26

Hello, Our company has the licensed commercial version of ChimeraX 1.10.1 running on RHEL 8.10. When trying to add the PhenixUI plugin from Toolshed, I get this error: ERROR: Could not find a version that satisfies the requirement ChimeraX-OpenCommand~=1.16 (from chimerax-phenixui) (from versions: none) ERROR: No matching distribution found for ChimeraX-OpenCommand~=1.16 The latest version of ChimeraX is 1.12, so I'm not sure what 1.16 is referencing. What do I need to do to be able to install the PhenixUI plugin? Thanks, JP ________________________________ Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] ________________________________

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Overlong bond displays in ChimeraX
by Vorländer,Matthias Kopano 26 Aug '26

26 Aug '26

Dear ChimeraX staff, For some mmCIFs, ChimeraX displays bonds that are physically unrealistic. For example, if you take PDB 9S2E ChimeraX draws a bond between residue /IN:52 and and /IN:154 (see screenshot). The PDB mol viewer (https://www.rcsb.org/3d-view/9S2E) does not display this bond. I noticed that structures in PDB format don’t show these bonds, so this is probably due to some connectivity records in cif format. I also have only observed this in nucleic acids, not proteins. Is this a bug that could be addressed? Thanks a lot and best wishes, Matthias [image.png]

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Letter of appreciation (Please read)
by Briana Salisteanu 25 Aug '26

25 Aug '26

Hello! I hope this e-mail finds you well ! :) Before you read this e-mail, no need to worry ; there were no issues or errors of the program I need help with ! My name is Briana and I am a 21 year old third year pharmacy student. I am writing you to thank you for the development of ChimeraX.This is the program that introduced me to the world of bioinformatics and molecular visualization.I come from Romania, from the University of Medicine and Pharmacy “Carol Davila” of Bucharest. I was not aware of the existence of such program.When my physiology professor (who is very much into programs of this kind and the continuous development of the bioinformatics domain) sat me down at the little laboratory’s computer and told me all about Chimera, I was fascinated.I remember exclaiming : “I can do this ?! There’s more to science than the typical lab life I’ve known for so long? More than the microscope..? “ .We were getting ready to start working on an article (that we are still in progress with, and my first article I get to write for ! ) for his post-doctorate. The first protein I worked with was ZLO4. This encounter I had with the digital world of science was the key to me discovering my passion for coding and much more.I decided to work harder.I started searching different master degrees across California that would fit my criteria for my dream job: a bioinformatician working in astropharmacy.I am currently studying how to use R and I’m making progress in Python everyday ! I work pretty well in YASARA and IGV too. This September I will start slow but steady to work on my bachelor’s thesis about Neuro-Endocrine Physiology and Microgravitational Adaptation in Female Astronauts.I believe strongly in the need for research and development in women’s healthcare.I will of course use Chimera X in my future work.You will make it possible for a girl from a small town in Eastern Europe to make a step forward into the big and sometimes scary world of STEM.You gave this girl a different perspective on the scientific world that she knew. I am currently in San Jose, CA visiting my parents.It’s Monday 24 August.Last Friday I came to San Francisco in the hope of meeting the team behind Chimera ! Unfortunately, no one was there and I was in the afternoon.I was so nervous and full of emotions , my eyes got watery haha ! For me it was the equivalent of going to the place where DaVinci painted the Mona Lisa ! : ) I will be here until Saturday night.My flight back to Romania is this Sunday sadly.I know you are very busy, but I’d like to get to thank you in person for your contribution to the scientific society. With respect, hope for the future and love, S. Briana-Maria.

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Re: Using ChimeraX for private research
by Tony Schaefer 20 Aug '26

20 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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