- ChimeraX-users - RBVI Mailing Lists

Exact meaning of RMSF (RMSD in sequence alignment)
by Alexandra Zahradnikova 17 Jun '26

17 Jun '26

Dear All, I was not able to find out what is the formula for calculating RMSF in the commans Sequences-> Headers-> Calpha. Does it calculate the RMSD per residue of distance between C-alpha of each of the associated sequence and the displayed sequence, or RMSD per residue between all of the associated sequences? Thank you very much in advance for explanation. Best regards Sasha

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ChimeraX 1.12 release
by Elaine Meng 12 Jun '26

12 Jun '26

UCSF ChimeraX version 1.12 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.11 (December 2025) include: - OpenFold3 structure prediction - Boltz server capabilities - cartoons with straight cylinder helices (alternative to curved tube helices) - 3D-SNFG glycan representations - Match->Align to create a multiple sequence alignment from a 3D superposition - label residues with color-coded grids of amino acid prevalences from an associated multiple sequence alignment in Profile Grid - Find Cavities options to include cofactors, restrict search to box - trajectory clustering - commands to reproduce clipping plane positions - Mutation Scores tool for analysis of deep mutational scanning results For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, 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

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Re: nucleotide tube/slab or slab for modified nucleotides
by Daniel Larsson 11 Jun '26

11 Jun '26

A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position). Regards, Daniel From: Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson(a)icm.uu.se> Date: Wednesday, 13 May 2026 at 14:48 To: chimerax-users <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: nucleotide tube/slab or slab for modified nucleotides Hi Elaine, Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header: loop_ _chem_comp.id _chem_comp.mon_nstd_parent_comp_id 2MA A 2MG G Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct. Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly. Regards, Daniel From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply to: chimerax-users <chimerax-users(a)cgl.ucsf.edu> Date: Tuesday, 12 May 2026 at 17:32 To: Daniel Larsson <daniel.larsson(a)icm.uu.se> Cc: Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides Hi Daniel, In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate. 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. [cid:image001.png@01DCF82D.773F82E0] There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago. 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 May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work. > > 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 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. _______________________________________________ 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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UniProt ID detection and display from mmCIF files
by Samuel Nitz 10 Jun '26

10 Jun '26

Hello, I’m adding metadata to a large set of mmCIF files coming from a large-scale AlphaFold prediction effort. The goal is to have descriptions for each polypeptide chain visible when opening the file in ChimeraX. Adding descriptions is easy via the _entity.pdbx_description parameter. However, I can’t figure out how to add UniProt IDs so they show up in their own column, which is usually the case for files I’ve downloaded from the AlphaFold database or PDB. I’ve tried editing struct_ref and struct_ref_seq , but ChimeraX still won’t display the UniProt IDs. How do I do this? Version information: mmCIF dictionary: mmcif_ma.dic 1.4.5 ChimeraX: version 1.10 (2025-06-26) Thanks for your help! Sam Nitz PhD candidate, Rock lab Rockefeller University

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Changing Chain IDs in ChimeraX
by Parvate, Amar D 10 Jun '26

10 Jun '26

Hi My name is Amar and I am working on the structure of a phage tail complex. I have multiple dodecameric assemblies within the tail complex. Is there a way to change/name chain IDs from say P1 to P12 in chimeraX so that they are all read and rendered? Can I make ChimeraX read chains beyond P9 when I have numbered them from say P1 to P12? Coot reads it fine but ChimeraX gets confused after P9 (image attached). I cannot select chain "P12" or any residue/sidechain in it [cid:image001.png@01DCF8BD.9D7AF260] Best Amar

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Chimerax questions
by McCune, Christopher 09 Jun '26

09 Jun '26

Hi, I have a few questions regarding the software. Is it supported by Windows 11 enterprise? Is it possible to install it in Program Files or program files x86? Does the installation do anything with the app data folder? Are all the executables and dependencies up to data with their code signing? Are there silent install switches available? Are there silent uninstall switches available? Thank you, Chris McCune Desktop Engineer Department of Medicine, School of Medicine University of Maryland, Baltimore 100 N. Greene St. RM 201 http://www.medschool.umaryland.edu/medicine/IS/

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Create pbonds or distances in different groups
by Kai Cai 09 Jun '26

09 Jun '26

Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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good day, for information.thanks
by PIERALISI CLAUDIA 02 Jun '26

02 Jun '26

Hi,my name is claudia pieralisi,I' m a student in specialistic course of degree in molecular and applicated biology at politecnic of marche university Italy, From a lot of time I am trying to put the Chimera X download in my personal computer Chrome Os -linux it is an old computer but very right and I use it with a lot of happiness. But I cannot to do it because the files are not supportated . Can you tell me what is the file of chimera is right? The link. Thanks see you soon Claudia Pieralisi

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ChimeraX Will Not Open After Installation on My HP Laptop
by PRIYANSHI . 01 Jun '26

01 Jun '26

Dear UCSF ChimeraX Support Team, I am having trouble running ChimeraX on my laptop. I successfully downloaded and installed the software, but it does not open when I try to launch it. When I click the ChimeraX icon, I only see the loading/buffering cursor for a few seconds above the desktop icon, and then nothing happens. The program never opens, and no error message is displayed. My laptop specifications are: - HP Laptop - Processor: AMD Ryzen 7 5700U with Radeon Graphics, 1.80 GHz - Installed RAM: 16.0 GB (15.3 GB usable) - Graphics: AMD Radeon(TM) Graphics (496 MB) - Storage: 159 GB used out of 477 GB - System Type: 64-bit Operating System, x64-based Processor - Operating System: Windows (64-bit) I have already tried multiple troubleshooting methods suggested by ChatGPT and Google Gemini, including reinstalling the software and other recommended fixes, but ChimeraX still does not open. Could you please advise me on: 1. Whether my system meets the requirements for ChimeraX? 2. Whether there are known compatibility issues with AMD Ryzen 7 5700U or AMD Radeon Graphics? 3. Any additional troubleshooting steps I can try? 4. Whether there is an alternative version or installation method that may work better on my system? I would greatly appreciate your guidance. Thank you for your time and assistance. Kind regards, Priyanshi

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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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