March 2026 - ChimeraX-users - RBVI Mailing Lists

addh to only parts of a model?
by Alexis Rohou 01 Apr '26

01 Apr '26

Hi all, As specified in the documentation, in command addh, "Hydrogens are added to entire atomic model(s) even if only parts of models are specified." Given how specifically this is stated, I'm guessing there was a good rationale for doing it this way. However I am facing a situation where I'd really, really like to add hydrogens only to waters (which were added by Servalcat). For reasons that I haven't got to the bottom of, addh adds hydrogens in the wrong places in a ligand I'm working on (a peptide with a mixture of natural and non-canonical amino acids, though I'm almost certain I've observed this behavior with other, less exotic, ligands). So: what is/was the rationale for not allowing users to add hydrogens to only parts of a model? How would the developers feel about a pull request adding an option to override this behavior and only add hydrogens to the spec supplied by the user? Cheers, Alexis

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Question about multiple sequence alignment after structural superimposition in ChimeraX
by OLIVA MIGUEL, BALDOMERO 31 Mar '26

31 Mar '26

Dear ChimeraX Team and Community, First, I would like to apologize if my question is redundant. I have only recently joined the community and may have missed previous discussions on this topic. I have been a user of Chimera on macOS, but with the most recent macOS updates, I have encountered compatibility issues that have led me to transition to ChimeraX. I am currently adapting to the new interface and commands, and I appreciate the many improvements it offers. However, I am missing a feature that I frequently used in Chimera: the ability to obtain a multiple sequence alignment after superimposing several structures using MatchMaker. This functionality was very useful in my workflow. I would like to ask whether there is an alternative approach in ChimeraX to achieve this, or if there are plans to include similar functionality in future updates. Thank you very much for your time and assistance. Baldo Oliva -- -- --------------------------- e-mail:baldo.oliva@ <e-mail%3Abaldo.oliva(a)gmail.com>upf.edu Baldo Oliva Miguel, PhD Structural Bioinformatics Laboratory (GRIB-IMIM) Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB) C/ Doctor Aiguader, 80. Barcelona-08003, Catalonia, Spain (EU) Tfn: 34-933160509 Fax: 34-933160550

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Suggestion
by Samo Lešnik 30 Mar '26

30 Mar '26

Dear developers, I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance. Best regards, Samo

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color the inside of ribbon helix differently
by Daniel Larsson 30 Mar '26

30 Mar '26

Hi ChimeraX team, I would like to color the inside of alpha helices in a different color from the outside, which is a standard feature in PyMOL and the original Chimera program: https://pymolwiki.org/Cartoon_highlight_color https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribinsidecolor.html But my understanding is that this is not currently possible in ChimeraX. I found some old mailing list threads on the topic and this 5-year-old open feature request ticket with priority set to low: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719 Based on comments from the developers, it seems as if implementing this feature is not very straight-forward with the current ribbon rendering engine. Still, I hope you will elevate the priority and put it on the road-map for future releases as it greatly improves visibility and 3D-feeling of large ribbon-style protein structures. It would add another important tool for users of your excellent software. Best regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChopChopMF — official user guide now available
by Lukas Bauer 30 Mar '26

30 Mar '26

Dear ChimeraX community, An official user guide for ChopChopMF is now available. ChopChopMF is a ChimeraX plugin designed to streamline protein structure analysis — providing a GUI-based workflow for mapping sequence alignments, mutations, and protein-protein interfaces directly onto 3D structures, without requiring extensive command-line expertise. The user guide covers installation, usage, and practical workflows: https://lukasinscience.github.io/ChopChopMF/ The plugin can be installed directly from the ChimeraX Toolshed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxchopchopmf Feedback and suggestions are very welcome. Best regards, Lukas

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Question about clipping and transparency
by John Watters 30 Mar '26

30 Mar '26

Hello All, I am experiencing an issue when I am trying to make a movie of a series of coupled atomic models and volumes overlaid on top of each other. I cannot seem to make what I believe is called the "surface cap" transparent when I have clipped into a volume and I am showing/changing the volume. When I call the transparency command in ChimeraX itself (without the script running) it works as it should and makes the surface cap transparent, but in the movie-making script it seems like the transparency command is having no effect? Do you have any suggestions on how to deal with this? Thank you! Example .cxc code block attempt clip off; clip near -24.984; transparency #1.1 90; ######################### hide #!*.*; hide #!* models; show #!1.2 models; #show volume show #!3 models; #show atomic model transparency #1.2 90;transparency #1.2.1.1 90; wait 3 hide #!*.*; hide #!* models; show #!1.3 models; show #!4 models; transparency #1.3 90;transparency #1.3.1.1 90; wait 3 ######################### Best, John

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How to generate an alignment to color by conservation
by Victor Ruiz-Arroyo 25 Mar '26

25 Mar '26

Dear ChimeraX staff, I am trying to make a representation to display the conservation using a color scale similar to this tutorial: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-… I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file: [image: image.png] However everytime I try to open it in chimeraX I get this matrix-like window: [image: image.png] Which is different to what I would expect based on the tutorial. In fact, if I download the .ali from the tutorial, I see the correct alignment window. I have tried different alignment formats without success, and I still get the "matrix window". What software and format do you recommend using in Chimerax? Best Victor

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chimerax-trimmings update
by Oliver Clarke 25 Mar '26

25 Mar '26

Hi all, For anyone using chimerax-trimmings, I gave it a bit of an update: https://github.com/olibclarke/chimerax-trimmings/ I reorganized it and cleaned it up, added more documentation, and took advantage of the new "synopsis" option for aliases to add a help strinng for each alias, so you can access usage info from the command line (typing help or usage followed by the alias name). I also added function keys to toggle shown models on and off, and to toggle shown maps on and off, as well as function keys to cycle through lighting presets, and a function key to cycle through model display options. Hope they are useful to some folks, let me know if so! Cheers Oli

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Color PAE plot from structure
by Pim Huis in 't Veld 19 Mar '26

19 Mar '26

Dear ChimeraX team, I am colouring a PAE plot from a predicted multiprotein structure. From: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/alphafold.html *Color plot from structure – color the plot to match the 3D structure where the pair of entities represented by an X,Y point have the same ribbon color; show the rest of the plot in shades of gray* I would like to use the correct values of the *shades of grey* to make a legend for the plot. Is there a way to see these? Is it possible to include the used palette info on the page above (as for rainbow and green)? Ideally, I would also like to change these shades of grey to have something a bit "steeper" (for example: 0 black, dark grey 5, grey 10, light grey 15, white 30). Is this already possible, or can it be added as a new palette or -ideally- as a customisable feature? Thanks a million! Pim

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Re: Easier way to reverse direction of PDB file?
by Guillaume Gaullier 18 Mar '26

18 Mar '26

Hi Mrinalini, Let's try to keep the list in CC, so the messages get archived and can help others. :-) It is difficult to understand your message without a visual. I don't know what you mean by "the stems of the proteins". But whatever it is that is going clockwise or counterclockwise, the fact that you are using these terms suggests to me that you are seeing different chiralities. I have seen it once that ab initio reconstruction followed by heterogeneous refinement produced classes of opposite chirality. This is indeed surprising, but not impossible if the starting 3D references have very low resolution (or are heavily low-pass filtered at the first iteration of the job). If you look at both maps side by side and they are mirror images of each other, then only one is a correct representation of your molecule: the one with right-handed alpha helices. (Unless you happen to work on mirror proteins made of D-amino acids, and decided to collect cryoEM data on a mixture of natural and mirror protein; but that would be a poor choice of experimental design, as it would make the image processing intractable to assign the particles to their true class.) Good luck with your project! Guillaume ________________________________ From: Mrinalini Ramanan <mrinalini.ramanan(a)gmail.com> Sent: Wednesday, March 18, 2026 5:27:46 PM To: Guillaume Gaullier Subject: Re: [chimerax-users] Easier way to reverse direction of PDB file? Dear Guillaume, Thanks for this quick yet thorough reply. Is it also possible to get maps with the wrong handedness if I have the main map going in a counterclockwise direction, and then maps from 3dva or 3d classes from this main map being in a clockwise direction? Only one of the classes is in a counterclockwise direction that matches the main map, the others are in a clockwise direction. I guess my question is regarding directionalities vs. chiral center: can two different directions result from the same chiral center? I've done vop flip on the maps and lined them up so that the stems of the proteins are aligned (with fit #1 in #2, and some with emailing), but the resulting cap directions are clockwise / counterclockwise. Thanks in advance for your help, Mrinalini Mrinalini Ramanan https://www.thehonestrational.com<https://www.thehonestrational.com/> On Wed, Mar 18, 2026, 4:54 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello Mrinalini, When reconstructing a 3D volume from 2D projections in cryoEM image processing, there is a 50% probability of getting either chirality. It is relatively easy to visualize why if you cast shadows of your hands: you can easily make the shadow look the same with both your right and left hand as the object casting it, despite your two hands not being the same in 3D due to chirality. But natural proteins only have L-amino acids, their alpha helices are right-handed, etc. So the correct solution in your case is not to build a model into a map of the wrong chirality, because the only way it would work in terms of stereo-chemistry would be with D-amino acids. You simply need to mirror the map. In ChimeraX, assuming your map is loaded as model #1, this command will mirror it: volume flip #1 (The resulting mirrored map will only live in your ChimeraX session, so if you want to keep it, you need to save it as an MRC file.) There is also a job to mirror a map in CryoSPARC, if this is the program you are using to process your data: https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/util… (this is the option "flip handedness" in this job). To tell chirality only from a map, in general, you need sufficient resolution to trace the backbone, and a protein containing alpha helices: then you can determine whether they are right-handed (the correct chirality) and invert the map if they are not. Some particles have chiral features that can be identified at much lower resolution (for example the super-helical turn of DNA around nucleosomes). But it is not always easy to tell depending on particle and resolution. If auto-building programs like ModelAngelo fail or produce many short disconnected fragments when applied to a good-looking map, this is often a sign of wrong chirality. I hope this helps, Guillaume ________________________________ From: Mrinalini Ramanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Wednesday, March 18, 2026 3:23:48 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Easier way to reverse direction of PDB file? Dear Chimerax community, I have a molecule that has a clockwise directionality for some cryoem maps, and a counter-clockwise directionality for some maps. I see this difference in directions even after fitting each map with the fit #1 in #2 command, and am now trying to build in each map. In order to create a PDB file with both directionalities, I used PyMol to do alter_state 1, obj, y = -y, rebuild, and then exported the new molecule. Is there a command in Chimera or Chimerax to do the same operations? I tried using matrix invert to no avail. Sincerely, Mrinalini VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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