- ChimeraX-users - RBVI Mailing Lists

tools for ligand-receptor interactions
by Elaine Meng 09 Oct '25

09 Oct '25

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > Hi Vojo, As per the Contact Us page <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> ...to ask questions you would use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again. I don't know what you mean by "on the site" since there is no webform for questions, only this email address. You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity). That's most of it. Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > > Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies... >

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Append ligand coordinates from one PDB to another
by George Tzotzos 08 Oct '25

08 Oct '25

I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions. George

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Issue in displaying pdb in chimeraX
by Rayees Mattoo 07 Oct '25

07 Oct '25

Hi, I merged two molecules in coot and generated a merged.pdb file. However, upon displaying in ChimeraX part of my model is cartoon and part of it displays as worm, see the attachment. After running dssp I can fix it, but I want it to display as cartoon by default. Anything I need to edit in the merged.pdb file? Best Rayees

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Modeller interface
by Alexandra Zahradnikova 07 Oct '25

07 Oct '25

Hi All, Today I am getting problems when trying to model loops with Modeller. Repeatedly (on different structures), the following error occurs: modeller refine 1/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standardException in thread Thread-33 (_run_function): Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function func(*args, **kw) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0). Is it a problem with the Modeler server? How can I find out in the future whether there is a problem with the server or the problem is in my input structure? Thanks in advance. Best regards Sasha

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Re: [Chimera] local resolution map colors
by Elaine Meng 06 Oct '25

06 Oct '25

I can't tell anything from the image, since I have no idea what your filenames mean. All I can say (again) is you have to open both the original map and the local resolution map, show the original map as a surface, and use the local resolution map values to color that surface. Elaine > On Oct 3, 2025, at 2:32 PM, Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> wrote: > > Hi Elaine, > > Thanks for your reply. Attaching the new screenshot here. This shows that the map values are 0.1095 all over. Please let me know if I can give any additional information. > ~Shatabdi > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, October 3, 2025 2:20 PM > To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera] local resolution map colors > !-------------------------------------------------------------------| > This Message Is From an External Sender > This message came from outside your organization. > |-------------------------------------------------------------------! > > Hi, > This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. > > Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > > Hi, > > > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > > > Thanks! > > > > Shatabdi Roy-Chowdhury, PhD. > > Cardiovascular Research Institute > > University of California, San Francisco > > > <Screenshot from 2025-10-03 13-56-32.png><Screenshot from 2025-10-03 13-56-51.png>> _______________________________________________ > > Chimera mailing list -- chimera(a)cgl.ucsf.edu > > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu > > > <Screenshot from 2025-10-03 14-29-30.png>

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Issue with the coordset slider in chimeraX
by jeandidier.marechal＠uab.cat 05 Oct '25

05 Oct '25

Hi everyone, I am starting to take steps into ChimeraX handlers of MD simulations. So far, there have been no problems loading the starting PDB file and the trajectory. However, I am unable to make the coordset slider work. I always have the minimal version with the frame slider, the snail, and the recording button. Nothing happens when running the coordset slide #number_of_the_model. So, I can not make distance plotting and so on. I tried different versions of the software, including the latest daily build and the most recent production release. Thanks a lot for telling me what I do wrong and, if not readily implemented, please apologize for my impatience ;-) Cheers JD

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04 Oct '25

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Save centroids in scene coordinates
by Andrew Kennard 03 Oct '25

03 Oct '25

Hi there, I have aligned a bunch of models with matchmaker, and then I defined centroids for each model with `define centroid`. I would like to export those centroids for further analysis (trying to see the spatial relationship between chains B from each model when all models are aligned on chain A). However, the only way I could figure out how to do it was to press "Save Info..." in the Structure Measurements window. This text file reports the centroids in the model coordinate system for each model. But because I aligned the models with matchmaker, I'd rather have the centroids in the scene coordinate system. I am not sure how to do this transformation and export all the coordinates (~dozens of models). The only other option I found that might work was the `getcrg` command which I could use to save the coordinates to the Log, but then I will have to save the log as an HTML and parse that, right? Is there any more straightforward way? Alternatively, is there a better way to define centroids (ideally programmatically) so I can extract them from Chimera easily in scene coordinates? Perhaps the measure center command is the thing I should be using? Thanks a bunch! I'm running ChimeraX v1.10.1 (2025-07-24) on Mac OS 15.6 Sequoia Thank you!! Andrew

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de novo octahedral assembly of AlphaFold-generated ferritin monomers
by jmcquaid＠ucsd.edu 03 Oct '25

03 Oct '25

Hi folks! I would like to use "Sym # O" to model how a novel marine ferritin might assemble into an octahedral nanocage. Like ferritin, this marine ferritin is thermostable and has a size consistent with a 24-mer, but the AA sequence is too divergent to use 'matchmaker'. I've noticed that if I create a fold model of human ferritin (1FHA) with AlphaFold and import it into ChimeraX, the 'sym # O' command generates a 24-mer hairball rather than an octahedrally-coordinated sphere. If I 'fetch' the same 1FHA protein directly from PDB, the spherical structure is correctly assembled. What additional commands might be needed to help ChimeraX correctly assemble an AlphaFold-generated 1FHA monomer into the canonical ferritin cage? Chimera used to have a 'group 432' command, but I see this is not currently supported. Thanks in advance! Knowing how to correctly assemble something known like human ferritin will greatly help in assembling something unknown like a marine ferritin. Best Regards, Jeff McQuaid, Scripps Institution of Oceanography

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Re: [Chimera] local resolution map colors
by Elaine Meng 03 Oct '25

03 Oct '25

Hi, This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > Hi, > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > Thanks! > > Shatabdi Roy-Chowdhury, PhD. > Cardiovascular Research Institute > University of California, San Francisco > > _______________________________________________ > Chimera mailing list -- chimera(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu

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Defining pdb chain ontologies
by Pranav Shah 30 Sep '25

30 Sep '25

Hi Team, I am writing to inquire about the functionality of ChimeraX, specifically concerning multi-subunit complexes with multiple chains of a single protein (e.g., PDB 4v7q). I am wondering if there is a feature that allows for manipulating chains by assigning them to functional ontologies. For instance, with the 4v7q example, I would like to be able to execute commands such as: color #1 "vp4" red `mm #1/"vp4" to #2/"vp4" These ontologies could be grabbed from the cif file and if the user decides define their pwn ontologies/groupings. If such a feature does not exist, would you consider exposing such a feature to the user? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Orient many tetramers
by Alexandra Zahradnikova 30 Sep '25

30 Sep '25

Hi I have a set of tetramers created by AlphaFold. They are randomly oriented. In order to measure their pore size in a third-party program, I need to orient them with their z axis pointing in the z direction. I can orient them with respect to the screen, but I don't know how to save this view orientation (i.e. so that the z axis in the pdb file goes vertically). Is there any way how to do it? The switch in the "save" command specifying whether to use transformed or untransformed coordinates does not make any difference, and the file is always saved in the original orientation. Best Sasha

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Suggestion for viewdock
by John Irwin 29 Sep '25

29 Sep '25

Hi Team We love viewdock. We would like to suggest allowing hotkeys for adjusting status e.g. for prioritization so that we do not need to mouse all the way down to click to change status. We think this might be a small change with a big usability and productivity impact. Thank you John John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

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Just a Big Thank You
by Esmaeeli,Reza 25 Sep '25

25 Sep '25

Dear ChimeraX Developers, This is Reza and I’m a computational chemist and protein designer. I’ve been a long time user of Chimera and now ChimeraX. Among many visualization programs that I have tried extensively including PyMOL, VMD, Maestro, ChimeraX has remained my favorite. I just wanted to take a moment and write this email just to say thank you for your amazing work. Even though it is free for academic users, this email is the least I should do after so many hours that I have enjoyed using it. The interface is great. The diverse set of features and modules are awesome. And the command line and scripting capabilities are so intuitive and easy to use. Can’t wait to see what comes next. Best Regards, Reza ChimeraX 1.10.1 on macOS Tahoe

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Re: [Chimera-users] Mapping conservation onto a structure
by Elaine Meng 25 Sep '25

25 Sep '25

Hi Shelley! Chimera and ChimeraX are two separate programs, so there are various differences. The email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu is CC'd here. I'll answer for ChimeraX since that's what you're using -- ChimeraX has a Sequence Viewer tool which is basically the logical equivalent of Chimera's Multalign Viewer, see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> See also the detailed tutorial on using ChimeraX to map conservation from a sequence alignment onto structures: <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 25, 2025, at 8:36 AM, Shelley Copley via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? > Thanks! > Shelley

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Is there a way to download a pdb and it's associated density map in one command
by Samuel Haysom 24 Sep '25

24 Sep '25

Is there any way I can fetch a pdb file from the web (e.g. $ open 1X2Y) and then also automatically fetch the associated cryoEM map if there is one? Looking in the mmCif file, there is a flag for the associated emdb-map (e.g. in 5ljo the mmCIF file there is a _pdbx_database_related.db_id flag with the corresponding id. It would be useful if this could be added as a flag to the open command if it isn't already. I'm sure it is also possible in some kind of script but I'm not hugely familiar with how to script in chimeraX. Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Ligand center
by NUR AIDA SAKINAH 24 Sep '25

24 Sep '25

Hi ChimeraX teams, I want to search ligand center for docking analysis. What command do I need to use to retrieve the ligand center (x,y,z)? Example pdbid is 4yvv and the ligand is GBM. So i want the GBM's x,y,z coordinates. Thank you. Regards, Aida.

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Regarding the method used by chimeraX for SASA calculation
by Prathvi Singh 23 Sep '25

23 Sep '25

Hi Elaine, I have used NACCESS ( https://www.bioinf.manchester.ac.uk/naccess/nac_intro.html) to calculate the SASA for a protein. It used the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method to calculate SASA. I wanted to know whether chimeraX also uses the same method to calculate SASA or not. If not, then can you mention how the chimeraX method differs from the method used by NACCESS? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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About "Minimizing Structure" feature in Chimera
by Zheyun Wang (MED,124090655) 23 Sep '25

23 Sep '25

Dear ChimeraX developers: I am Wang Zheyun, a student in Chinese University of Hong Kong, Shenzhen. In my computational biology course, our professor demonstrated to us that the molecular structure (a file containing several water molecules) can be changed to an energy-minimizing structure using "Minimizing structure" function in Chimera. However, I cannot find this function in ChimeraX(1.10.1), and professor told me that these two are completely different softwares. Is this function available in ChimeraX? If so, may I know where it is? If not, will this be added to ChimeraX or is it deliberately deleted? Looking forward to your reply! Sincerely, Wang Zheyun

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Python API: locate_maximum logic
by nrajan53045＠utexas.edu 19 Sep '25

19 Sep '25

Hi there, I was hoping to implement something similar to the rigid rotation/translation optimization within fitmap due to its efficiency. I have some code which appears to implement the same logic as locate_maximum from your github, but is returning wildly different affine matrices than I expect. I just had a couple of questions regarding the logic: 1) locate_maximum receives an conversion matrix from world to voxel space (xyz to ijk) as one of its parameters from volume's matrix_and_transform function. I was wondering what this matrix actually is? I was tracing through the matrix_and_transform function and I couldn't really figure this out. I am currently assuming that the transform matrix is a 3 x 4 affine matrix: 1/v * (I | -O). Where v is the isotropic voxel size, I is a 3 x 3 identity matrix and O is a 3 x 1 vector representing the origin of the map. 2) Within each step of a segment, the following is done (from steps_to_maximum): ``` if step_types: for step in range(steps): calculate_step = step_types[step % len(step_types)] xyz_to_ijk_tf = xyz_to_ijk_transform * move_tf step_tf = calculate_step(points, point_weights, rotation_center, data_array, xyz_to_ijk_tf, ijk_step_size, metric, syminv = syminv, values = values, gradients = gradients) move_tf = move_tf * step_tf ``` In this loop, xyz_to_ijk_transform looks like the full conversion matrix from world to voxel space. But each iteration also multiplies it by move_tf before applying the step calculation, and then updates move_tf again with step_tf. At first glance, it seems like we’re reapplying the same full transform at every step... so why not just apply it once, instead of multiplying it repeatedly inside the loop? And then when we return to locate_maximum, move_tf is once again applied to the full conversion matrix. before continuing the iteration. I apologize if this is nitty gritty detail, but I would really like to make sure my logic is sound when I am implementing my version of this algorithm. Thank you for your time, Nikhil Rajan

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Generate a volume from a shape
by Guillaume Gaullier 18 Sep '25

18 Sep '25

Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. Thank you in advance, Guillaume 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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Guidance on SASA/RSA calculation in ChimeraX
by Kazi Sayeeda 16 Sep '25

16 Sep '25

Dear ChimeraX Support Team, I am currently using ChimeraX (v1.10.1) to study whether certain amino acid residues are surface-exposed or buried in my protein structures (WT and mutants from AlphaFold/NeuroSnap). To assess this, I measured solvent accessible surface area (SASA) with the following commands: measure sasa #1 measure sasa #1:92 measure sasa #1:562 This gives me the following SASA values (in Å²): * WT Ala92: 216.4 Å² * WT Gly562: 189.0 Å² When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å): * Ala (max ASA) = 129 Å² * Gly (max ASA) = 104 Å² I get relative solvent accessibility (RSA) values greater than 1: * Ala92: 216.4 / 129 = 1.68 * Gly562: 189.0 / 104 = 1.82 Since RSA should not exceed 1, I believe I am mismatching ChimeraX’s calculation settings with the MaxASA reference set. So my questions are: 1. What radii model and probe radius does measure sasa in ChimeraX use by default? 2. Is there a way in ChimeraX to directly assign per-residue SASA attributes and normalize them internally (so RSA values remain ≤1)? 3. If ChimeraX defaults differ from published MaxASA tables, would you recommend reporting only SASA values, or generating my own MaxASA reference values with ChimeraX for consistency? I would be very grateful for any guidance or documentation pointers so I can report values in a way that is consistent and interpretable. Best, Kazi Sayeeda PhD Candidate Dept. of Cell and Developmental Biology (Krendel Lab) SUNY Upstate Medical University Syracuse, NY 13210 sayeedak(a)upstate.edu<mailto:%20sayeedak@upstate.edu>

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Re: scan results for vr.ucsf.edu
by Tom Goddard 15 Sep '25

15 Sep '25

Hi Greg, The web site report for vr.ucsf.edu <http://vr.ucsf.edu/> you shared takes me to web site that requires a login if I want to see what links are broken. Tom > On Sep 15, 2025, at 6:04 PM, Siteimprove Reports <reports(a)siteimprove.com> wrote: > > > Hi there, > Greg Couch (gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>) wants to share a dashboard report with you. The report was generated from "DCI score dashboard" at 6:02 PM on 9/15/2025. > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > > > > > > > > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > © 2025 Siteimprove > Havneholmen 33, DK-1561 Copenhagen, Denmark >

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Display the bfactor value when the mouse goes over a residue?
by Vincent CHAPTAL 15 Sep '25

15 Sep '25

Hello, I'd like to know, in addition to residue name and model, the bfactor of a residue when the mouse goes over it. For example model#1.20/A PHE 1482 bfactor 120.7 Could you help me to do it? Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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AlphaFold3 structures coloured in ChimeraX
by Vladimir Saudek 12 Sep '25

12 Sep '25

Hello, I am using ChimeraX 10.1 to display the results of AlphaFold3 predictions. I observe a large discrepancy between the colour coding of the quality of the structure (pIDDT) displayed at the output of the AF3 server and ChimeraX (I use the command color bfactor #1 palette AlphaFold, 1 being thenumbero of the structure to colour). ChimeraX's colouring indicates that the quality of the predicted structure is substantially lower then than that of theAF3 server. Is there any possibility to get ChimeraX to display the AF3 server colours? Below is an example, right AF3 output, left ChimedraX. Best regards Vladimir

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