- ChimeraX-users - RBVI Mailing Lists

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

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

26 Aug '26

Hi Artie, Thanks a lot for the careful analysis! An additional complication with his is that we don’t actually know the sequence of the intron chain, as this is a steady state endogenous sample with lots of different sequences bound. Plus, it is a circular (or more accurate lariat shaped ) molecule with an internal covalent bond, so it’s a bit of a headache. I will try and get in touch with the PDB to try and resolve this. Thanks for the help, Matthias From: Artie Kushner <rtkushner(a)gmail.com> Date: Wednesday, 26. August 2026 at 11:34 To: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at> Cc: Greg Couch <gregc(a)cgl.ucsf.edu>; chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Overlong bond displays in ChimeraX Hi Matthias, Maybe this helps on the molstar side (it actually does draw something similar to what you show in chimerax, but it is not exactly a bond but more of a connectivity hint): ``` Mol* never infers a covalent bond from sequence adjacency. Two subsystems, both gated on geometry: Bond graph — intra-compute.js:findBonds(). Bonds come only from struct_conn, from chem_comp_bond (intra-residue only), or from a 3D neighbour search capped at DefaultBondMaxRadius = 4 Å. O/P has no entry in __ElementPairThresholds, so getPairingThreshold falls back to (1.52 + 2.0) / 1.95 ≈ 1.81 Å. A 168 Å pair never enters the candidate list. Cartoon/polymer trace — atomic-ranges.js:getAtomicRanges(). This is the direct answer. When seqId === prevSeqId + 1, Mol* does not trust it, it verifies: if (conformation.xyzDefined && !areBackboneConnected(riStart, riEnd, ...)) { polymerRanges.push(startIndex, prevEnd - 1); // add gap even for consecutive residues if they are not connected gapRanges.push(prevStart, residueSegment.end - 1); areBackboneConnected measures O3'→P for nucleic and requires < 3 Å. Both joins fail, so chain M is split into three polymer ranges. So: ChimeraX trusts the annotation, Mol* trusts the coordinates. ``` And regarding the model itself it just seems that you guys stitchhed the intron together awkwardly (which is not an indictment to you but to a labyrinthine cif format id say). ``` 1. The intron SEQRES contains only the modelled residues Every other polymer chain in 9S2E is annotated correctly: entity_poly_seq carries the full biological sequence, and unmodelled residues just leave gaps in label_seq_id. PRP8 declares 2335 and models 1979. Aquarius declares 1485, models 1369. Fifteen chains have author-numbering jumps, and in every one of them except the intron the jump sits on a real label_seq_id gap — so every viewer breaks the chain correctly. Chain M is the only chain in the whole entry where declared equals modelled: 61 of 61. So label_seq_id runs 1..61 with no gaps, which is a positive assertion that these are 61 chemically consecutive nucleotides. The corollary is the damning bit: pdbx_unobs_or_zero_occ_residues has zero rows for chain IN. There is nothing anywhere in the file recording that the intron is incomplete — except the author numbering, which is free-form metadata that software can't legitimately derive connectivity from. They deleted the evidence of the gaps by defining the entity as "what I modelled" instead of "what the molecule is". 2. The three fragments are stitched in the wrong order In label_seq_id order the fragments are auth 1–24, then 136–154, then 50–67. Biological 5'→3' would be 1–24, 50–67, 136–154. So even taking the concatenated sequence at face value, the declared polymer direction says U154's 3' end is bonded to U50's 5' end — running backwards through the intron. That's why the phantom bond is the 168 Å one and not one of the shorter possibilities. What it should have been Either declare entity 13 with the full intron sequence (≥154 nt), leaving label_seq_id gaps at positions 25–49 and 68–135; or split the three fragments into three separate struct_asym entries so nothing claims they're covalently continuous. The rest of the entry already does the first thing correctly, fourteen times over — so this looks like the intron chain was built and named by hand, separately from the rest of the deposition. ``` [image.png] Best, Artie On Wed, Aug 26, 2026 at 10:31 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Greg, Thanks a lot for looking into this and for the reply. I was wondering if you had any guesses why the mol viewer does not show this bond? In case anyone is interested, I attached a python script that detects and hides such bonds . Best, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Greg Couch <gregc(a)cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> Sent: Tuesday, 25 August 2026 21:41:37 To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Cc: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Subject: Re: [chimerax-users] Overlong bond displays in ChimeraX So what you are seeing is not a bond, it is a cartoon connecting the disjoint parts of a single Intron. According to the mmCIF file's metadata, those two fragments are next to each other. That a bug in the mmCIF file. And ChimeraX faithfully reproduces buggy data, otherwise, you'd never know. The PDB should have caught that error on deposition. It might be a bug in software used to refine the structure. Please continue to report problems like this. mmCIF files are relatively new, and we are still learning about how Analysis: The entity_poly table says that Intron entities have 122 nucleotides. The atom_site table's label_asym_id and label_seq_id values indicate that there is one instance of the Intron entity with its first 61 residues present. Adjacent nuceotides are implicitly connected. Gaps are indicated by gaps in the label_seq_id values, and there are none. As you observed, from the disjoint fragments in 3D, that information is not correct. Another clue is the auth_seq_values that range from 1 to 24 and 136 to 154. Since the 136 is more that 122, maybe it should really be two separate chains instead of one chain? Or maybe the numbering is wrong. Can't tell. Bad data. I'd recommend contacting the author and/or the PDB to get it fixed. HTH, Greg On 8/25/2026 4:34 AM, Vorländer,Matthias Kopano via ChimeraX-users wrote: 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] _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@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<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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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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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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