- ChimeraX-users - RBVI Mailing Lists

B-factor and error in distance measurements
by Charles Midgett 18 Aug '25

18 Aug '25

I have two structures of a protein solved to different resolutions, one pretty good and the second not so good, and I want to compare distances between congruent atoms in the structures. It occurred to me that I have no idea if the differences in the distances are within the positional error of the atoms or not. Therefore, is there a way to propagate the positional uncertainty in the B-factors into a linear distance uncertainty? Sincerely, Charles

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Multiple sequence alignment display
by Betancurt, Leonardo 18 Aug '25

18 Aug '25

Hello, I would like to display a multiple sequence alignment based on structure after match maker. I use the command ”mm #!1-4 to #5 showAlignment true” but ChimeraX shows multiple pairwise alignments, is there a way to create a multiple sequence alignment? Thank you, Leo Betancurt, Ph.D. Post Doctoral Researcher | Zatopek Lab<https://www.neb.com/en-us/research-labs/zatopek-lab?srsltid=AfmBOoqPDIvrCfa…> New England Biolabs Inc. 📞 (978) 380-7290 📱 (351) 350-4075 [signature_474729057]<http://www.neb.com/>

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Re: ChimeraX support: Alphafold contacts
by Elaine Meng 14 Aug '25

14 Aug '25

Hi Tony! There are lots of options in menu: Select... Contacts, so it rather depends on all of the specific settings that you chose. Here is the help for that GUI: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> To summarize in regard to your questions... If you are in the Chains tab, you have a choice to use atomic distance or buried surface area. If you chose atomic distance it is using all the atoms and doesn't care what is backbone or sidechain. It would be the minimum distance (closest pair). At any point you can just simply list the residues in the current selection, e.g. command info residues sel ... which will go to the Log but you could alternatively save to file, e.g. info residue sel saveFile ~/Desktop/contacts.txt If you are in the Atomic tab, then you have the choice to use VDW overlap (negative distance between VDW surfaces) or center-center distance as the main criterion. If using that tab, presumably you would have already selected one of the chains and then designate to limit the results to atom pairs where one of the atoms is selected. You don't have to go through GUIs. If you just want to list residues in one chain with any atom within some distance of any atom in another chain, you could use commands like the following to select protein residues in chain A within 5.0 Angstroms of protein residues in chain C. The "protein" intersections are because some structures have water, ligand, ions with the same chain IDs as the protein chains, but I wanted to only consider the protein. select (/A & protein) & (/C & protein) :<5.0 info residues sel If the chains were only protein anyway, or you wanted to include any nonprotein residues, could be simpler select /A & /C :<5.0 See command-line zone specification and combinations such as intersection (&): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> Again it is all atoms and the closest pair. 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 Aug 10, 2025, at 5:39 PM, Anthony Newcombe <anthony.newcombe(a)appliedbiopharm.com> wrote: > > Hello Elaine > > I have a commercial license of ChimeraX. Further to the email below, I have been using the menu and GUIs to select > contacts as described in your online message below > > https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… > > This highlights the residues, and returns ' 267 atoms, 264 bonds, 32 residues, 1 model selected' between chains A and C > > But is there a simple command to list the identified residues as an output that are within less than 5 Angstroms and may interact for chain A or chain C, ie > > LEU264 > SER265 > ALA266 > > Also one question regarding the atomic distance used, is this a max distance between side chains, or the distance between the peptide backbones? > > Thanks for the help and apologies if these are simple questions > > Many thanks > > Tony

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Assistance: ChimeraX morph
by Priyanka Abeyrathne 12 Aug '25

12 Aug '25

Hi, I have two cryo-EM models (PDBs) at neutral and acidic pH conditions, both containing 486 amino acids. I would like to compare them by calculating the RMSD per residue, and then generate a morphing animation between the two structures. I used the following commands in ChimeraX: 1. I aligned the two structures using MatchMaker: mm #1 to #2 showAlignment true 2. I clicked on one amino acid in the MatchMaker alignment results to highlight the aligned residues. 3. Then I used the command: select ~sel to select residues with an RMSD greater than 1 Å. 4. To visualize the atoms of the selected residues with high RMSD, I ran: display sel & protein 5. I then cleared the selection using: select clear 6. Finally, I attempted to generate a morphing animation using: morph #1,2 wrap true frames 60 However, this command did not work. Could you please help me troubleshoot this? Thank you. Kind regards, Priyanka

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Creating an AtomicStructure object (along with other atomic objects) from scratch using Python API
by nrajan53045＠utexas.edu 11 Aug '25

11 Aug '25

Hi there, I am new to ChimeraX and its python API. As I was looking through the documentation, I noticed there were some atomic data classes (AtomicStructure, Atom, Atoms, Residue). Say I have a PDB file with information about all the atoms in the model, am I able to simply create Atom objects from reading the PDB file and, consequently, add these Atom objects to an AtomicStructure object? The reason I want to do this is because I want to use the fitmap function while limiting any disk IO. So, opening the file in ChimeraX (even if using the no gui offscreen functionality) would not work. I thought of simply creating objects from scratch, but I am running into errors when instantiating them. Sorry if this is an obscure problem or if I was unclear. Thanks for your help! Best, Nikhil

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Not opening
by Davis, Jamaine 11 Aug '25

11 Aug '25

Hello, We are attempting to install ChimeraX 1.10.1 on a PC. We can install it, but it will not open. Can you provide assistance? Best, JSD

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Version of Boltz in updated ChimeraX
by Jacek Jagodzinski 11 Aug '25

11 Aug '25

Do I need to manually/separately update Boltz to ver2 from ver1 after updating to current ChimeraX 1.10.1 or is this handled while update is installed? Jacek

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Tailoring Boltz-2 ChimeraX Output for AlphaBridge server Circos Plot Submission
by Arun Gupta 09 Aug '25

09 Aug '25

Dear ChimeraX Team, I am currently working on visualizing interface residues using Circos plots via the Alphabridge web server, and I’m exploring ways to tailor the Boltz-2 ChimeraX output folder to serve as a compatible input format for Alphabridge web server (https://alpha-bridge.eu/) similar to the AF-3 output zipped folder. AlphaBridge<https://alpha-bridge.eu/> Zip file containing the AlphaFold resultSubmit job alpha-bridge.eu Despite successfully generating Boltz-2 outputs in ChimeraX daily build, I’m facing challenges in aligning the output folder with what Alphabridge web server expects for Circos plot generation. Could you kindly advise on: * Whether there is a recommended way to export or reformat Boltz-2 ChimeraX outputs for Alphabridge webserver compatibility? * Any scripts or workflows that facilitate this integration? Any advice on post-output work flow steps would be immensely helpful, as I aim to produce publication-quality Circos plot visualizations of interface residue networks similar to those demonstrated by recent AlphaBridge pre-print publication (DOI: https://doi.org/10.1101/2024.10.23.619601) Thank you very much for your support and for the fantastic tool you continue to develop for structural biology community. I look forward to your recommendations. Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ Tel: + 44 (0)1865 2612913

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Re: Post-translational Modification in Boltz Prediction
by Tom Goddard 08 Aug '25

08 Aug '25

Hi Xicong, You need to run that boltz command from a terminal, not from the ChimeraX command-line. Since you are on Windows you could use Windows Command Prompt, or PowerShell. I use a cygwin bash shell. Any of those will work. You are directly running the Boltz executable instead of using ChimeraX to handle the modified residue. Tom > On Aug 8, 2025, at 1:54 PM, Xicong Wang <xicongwang(a)brandeis.edu> wrote: > > Hi Tom, > I tried to enter the command in the command line, but it says that it is unknown. Did I miss something? My YAML file with phosphothreonine and phosphotyrosine is p38alpha - 2p.yaml. > Best, > Xicong Wang > <image.png> > > On Thu, Aug 7, 2025 at 6:38 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Xicong, >> >> As Elaine said ChimeraX does not currently have a user interface to modify residues in Boltz predictions. I have not had time to add that yet. But you can pretty easily add the modification to input file for Boltz that ChimeraX creates and run it from a terminal. >> >> Here is an example of how to predicted a protein with a phosphoserine, I used PDB 2PIL as an example. I ran Boltz in ChimeraX with a standard serine. Here is the input YAML file ChimeraX produced ~/Desktop/2pil/2pil.yaml >> >> version: 1 >> sequences: >> - protein: >> id: [A] >> sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK >> >> I copied this 2pil.yaml file to 2pil_sep.yaml and added a few lines to say make serine 68 a phosphoserine (3-letter code SEP): >> >> version: 1 >> sequences: >> - protein: >> id: [A] >> sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK >> modifications: >> - position: 68 >> ccd: SEP >> >> Then I reran the boltz command that ChimeraX used from a terminal changing the 2pil.yaml input file to 2pil_sep.yaml. The command ChimeraX used is in the ~/Desktop/2pil/command file >> >> $ /Users/goddard/boltz/bin/boltz predict /Users/goddard/Desktop/boltz/boltz_2pil/2pil_sep.yaml --write_full_pae --use_msa_server --accelerator gpu --no_potentials >> >> When that ran it put the resulting predictions in >> >> boltz_results_2pil_sep/predictions/2pil_sep/2pil_sep_model_0.cif >> >> so I open that prediction in ChimeraX and aligned it to my original PDB using ChimeraX command "matchmaker #3 to #1". Result is shown in the image below. The Boltz documentation page shows other ways you can modify the input .yaml file for instance to add templates or constraints between atoms >> >> https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md [github.com] <https://urldefense.com/v3/__https://github.com/jwohlwend/boltz/blob/main/do…> >> >> In the future I hope to provide ChimeraX user interfaces to allow those possibilities. >> >> Tom >> >> PDB 2PIL in tan, Boltz prediction with serine 68 in blue, Boltz prediction with phosposerine 68 in pink. >> >> <boltz_mod.png> >> >>> On Aug 7, 2025, at 8:36 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Sorry no, the ChimeraX tool to run Boltz does not have a way to define post-translational modifications. This issue is mentioned in the Limitations section: >>> >>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html#limitations [rbvi.ucsf.edu] <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/…>> >>> >>> Best regards, >>> 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 Aug 6, 2025, at 7:07 PM, Xicong Wang via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Dear ChimeraX developers, >>>> I'm trying to predict a structure with two phosphorylated residues using Boltz. Is there an option for me to do that in ChimeraX? I didn't find any options to let me do any post-translational modification on the protein sequence I entered. >>>> Best regards, >>>> Xicong Wang >>> >>> >>> _______________________________________________ >>> 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/ [mail.cgl.ucsf.edu] <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list…>

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Post-translational Modification in Boltz Prediction
by Xicong Wang 07 Aug '25

07 Aug '25

Dear ChimeraX developers, I'm trying to predict a structure with two phosphorylated residues using Boltz. Is there an option for me to do that in ChimeraX? I didn't find any options to let me do any post-translational modification on the protein sequence I entered. Best regards, Xicong Wang

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