May 2026 - ChimeraX-users - RBVI Mailing Lists

displaying pLDDT in same color as Alphafold server?
by Nakamura, Toru 29 May '26

29 May '26

Hello, I am not sure if this is the right place to ask, but I have tried and failed Chimera to display what resembles the AlphaFold server, and it seems that it is using a long color scheme. I typed “color factor #1 palette alphafold, but it does nothing, and the predicted aligned error & what is displayed is probably a different color scheme? What am I missing here? Thank you for your help! Toru [Screenshot 2026-05-29 at 6.30.14 AM.png][Screenshot 2026-05-29 at 6.30.45 AM.png] ==================================== Toru M. Nakamura, Ph.D. Professor of Biochemistry & Molecular Genetics ~~~~~~~~~~~~~~~~~~~~~~~~~~ University of Illinois at Chicago College of Medicine Dept. of Biochem. & Mol. Genet. 900 S. Ashland Ave. MBRB Room 2202, MC669 Chicago IL 60607, USA ~~~~~~~~~~~~~~~~~~~~~~~~~~ E-MAIL: nakamut(a)uic.edu Lab: https://nakamura.lab.uic.edu/

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Security scan complaining about ChimeraX Python component
by Kirshner, Dan 27 May '26

27 May '26

Hello: Sorry, we’ve got an annoying security scan. Here’s its complaint: Path : /Applications/ChimeraX-1.12-rc2026.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiohttp-3.13.1.dist-info Installed version : 3.13.1 Fixed version : 3.13.4 Potential Vulnerability : Component Is there some way for me to update the Python that ChimeraX uses? Thanks very much, —Dan

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regional minimization?
by Daniel David Richman 27 May '26

27 May '26

Hi folks, In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon? Thanks, Daniel

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Cellpack reading
by huybk81＠gmail.com 22 May '26

22 May '26

Hi, In Chimera, there is a cellpack plugin to open a cellpack file. Is there any particular reason that ChimeraX doesn't have an equivalent function?

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fitmap - search flipped map?
by Oliver Clarke 19 May '26

19 May '26

Hi, I would like to suggest a possible enhancement for fitmap that would be useful in cryoEM workflows - optionally searching both the original map, and a z-flipped copy. In cryoEM, we often obtain initial reconstructions using ab initio reconstruction, which may converge on either the correct or inverted hands, and at low resolution, it is sometimes difficult to distinguish which (if any) is a correct solution - often, unambiguous fit of an atomic model is helpful to confirm that one has a correct solution. Fitmap with global search (e.g. fitmap #1 in #2 search 100 radius 5) is useful to get an initial fit list. It would therefore be convenient if fitmap had an option to automatically test the fit of a model vs both the selected map and a z-flipped copy. We do this now by pre-flipping the map and doing two searches (one against each copy), but when all the classes are loaded from a classification job this can become a bit unwieldy, in terms of keeping track of which map ID corresponds to the flipped copy of which map. Cheers Oli

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Does ChimeraX incorporate bond geometry or torsional state into atom display?
by Wes Dennis 19 May '26

19 May '26

Hi, My nameis Wes Dennis and I am a retired Geophysicist who is just interested in stuff. I am trying to understand what I am seeing with two ChimeraX images. I applied identical atom-name based coloring commands to the same residue range in two different crystal structures of the same molecule — backbone atoms colored blue, aromatic base atoms colored yellow. The visual result is strikingly different between the two structures. In one, blue color appears to spread into the base panels — a structure in which torsional stresses are present. In the other, where torsional stresses are absent, the base panels are clean yellow with no blue intrusion. My question: does ChimeraX incorporate any geometry-dependent information — bond angles, torsional state, idatm type reassignment based on local environment — into atom rendering or classification that would cause identical coloring commands to produce visually different results across structures? Or is ChimeraX rendering purely atomic positions as recorded in the mmCIF file with no geometry-based modification? Two Images attached Thank you for your help Wes Dennis ------------------------------

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Fwd: opening cryoEM SPA maps using "volume" view mode
by Eric Pettersen 19 May '26

19 May '26

> Begin forwarded message: > > From: Jonathan Paul Remis <jpremis(a)berkeley.edu> > Subject: opening cryoEM SPA maps using "volume" view mode > Date: May 18, 2026 at 4:36:10 PM PDT > To: chimerax-bugs(a)cgl.ucsf.edu > > Hello wonderful people that build and maintain Chimera! > > > I have run into a bit of an odd observation which when compounded with some basic biochemistry has left me scratching my head. Essentially, when I open one of our SPA volumes in chimerax and choos "volume" in the volume viewer I am able to see a single bright spot in the volume. If I process our data with C2 symmetry we see two bright spots. > > I had thought this was biologically relevant but I opened up a couple more structures from our lab and other labs and see this is pretty common. Please see the attached images and you can see ApoFerritin has 24 bright spots, and Aldolase has 4. > > In the case of my sample - hemoglobin - the bright spot co-localizes with a iron element in the structure. I want to believe this has something to do with the density/scattering of the Fe but am at a loss for why we would not see 4 of them. Hemoglobin has 4 heme centers and 4 Fe atoms. > > Thank you in advance for any suggestions or support you can provide. > > Thanks, > Remis > > > > > > > > > > > -- > Jonathan Remis > Scientific Engineer > Müller Lab > University of California, Berkeley

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pdb file problems and chimerx
by Steven Brawer 15 May '26

15 May '26

I will be using ChimeraX much more extensively this fall, and I think the answer to the question below might be useful (and not just for me). Does there exist some list (or lists) of common pdb file errors? One probably can't cover all possibilities, but perhaps there are some common ones that one could find automatically by writing a python program to examine the file. (Perhaps some programs already exist.) Recently there was a case of misplaced spaces and also of duplicated lines. Presumably one could (perhaps) add a search for the correct number of atoms in each residue. What about the existence/presence of water or heavy ions? Perhaps searching for unexpected atom-atom-atom angles or bond lengths (or even separations)? Perhaps an AI agent might be trained? Thanks Steve Brawer

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Covalently attaching unusual ligands
by TheWildBynapie 15 May '26

15 May '26

Hi there, I'm a bioinformatics UCT student and we've been given an assignment to solve a protein structure. Everyone has been struggling with this step and I've tried many many ways to get this to work in ChimeraX, but I get new errors every time so I'm asking for help. Sorry for the long question, but I would *highly* appreciate help at this point (and so would my class - so if I get an answer you'll be making ~30 people very happy, not just 1!) Essentially this ligand has a sulphur that makes a thioester to Cys 146, our professor said we should remove the Cys sulphur and then combine the ligand and the remainder of the ligand into one residue and name it 'AKG.' We have a dimer so we also do this in 2 places. We need to refine this using ISOLDE, which is where most of my problems appear. Then he says we can use 'AKG.xml' in residue parameterisation so ISOLDE will accept our residue. Currently the way my pdb is layed out causes chimera to only render the ligand part of AKG but not the Cys part. I don't know why, and more importantly my general understanding of how ChimeraX reads pdb files is lacking. *So I suppose finally my actual question*: what do I need to do to make it so ChimeraX renders the residue correctly, and ISOLDE accepts AKG.xml and can actually run a simulation on this pdb? I've attached: 1: AKG.xml (for residue parameterisation) 2: 5 - refine1.mtz (the electron density map data) 3: 6c - part of AKG missing.pdb (the current pdb I'm working with where the Cys part of residue 146 isn't rendered) 4: 6b - pre-covalent linking.pdb (the latest copy of the pdb I could get running in ISOLDE simulations. This has the protein dimer and 2 ligands as 3 separate models. I'd already deleted the Cys's Sulphur here so it's more like an Ala in this case) Sorry for such a massive email, but I wanted to be as specific as possible with my problem. If you could provide me some help it would be extremely helpful. Sadly our lectures for this module are over and getting our lecturer to explain anything is virtually impossible. Thanks so much, Byron (and the rest of my class to be honest)

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Can you export results of your work in Chimera as a pdb file
by Vojo P Deretic 13 May '26

13 May '26

Can you export results of your work in Chimera (for example after matching and aligning structure) as a .pdb file? Vojo Deretic, Ph.D. Distinguished Professor Department Chair, MGM Director, AIM Center University of New Mexico School of Medicine vderetic(a)salud.unm.edu<mailto:vderetic@salud.unm.edu> Follow AIM, NIH-funded Center of Biomedical Research Excellence: https://www.autophagy.center/ X/Twitter @AIM_autophagy Don’t forget to acknowledge the AIM Center (Autophagy, Inflammation and Metabolism) and the CoBRE grant in publications The AIM Center is supported by NIH grant P20GM121176. For citation options see suggested wording at https://www.autophagy.center/

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