- ChimeraX-users - RBVI Mailing Lists

How to replace ss_id for a secondary structure region?
by Rayees Mattoo 25 Jul '25

25 Jul '25

Hi, I have a region in my structure (res 208-229) which is displayed as a discontinuous helix when I am certain it is a continuous helix. I want to modify the pdb file to consider it as a continuous helix using chimeraX. I used the following commanlines: settatr #1/K:208-229 res ss_type 1 setattr #1/K:208-229 res ss_id 999 It works. However, I believe the command assigns the same region with a new unique ss_id (999), leaving the original ss_id intact. If I want to replace the the original ss_id with a new sequence range (res 208-229) how would I do that? Also, is there a way to directly text edit pdb file secondary structure list in ChimeraX? Best Rayees

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ChimeraX color fromcartoon error
by Prafful Sharma 25 Jul '25

25 Jul '25

* Dear ChimeraX Developer, I was recently trying to color a model in chimeraX based on a similar model with the same chain IDs and residues, and so I was using the command color fromcartoon #1 target #2 as specified in the documentation however I am receiving an error that says " Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword". I assume it is asking me to add a specific color name/code, but the other models have many different colors. I tried multiple turnarounds and even took help from different AI models, but still could not solve the error. I therefore think the functionality is not active, or there is some issue with I am not able to figure out. Can you please let me know if this functionality is working, or if there is any other way I can do this? Thank you for ChimeraX and your kind help! Prafful Sharma Ph.D candidate, TH lab | Structure, function, and regulation of protein synthesis Dept. of Developmental Biology and Genetics, Indian Institute of Science, Bangalore 560012

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Obtaining a list of residues that are solvent-accessible
by Gracia Mazuca, Luis Antonio 24 Jul '25

24 Jul '25

Hello, I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results. I look forward to hearing from you. Thank you very much in advance. Best, [cid:25bde0d5-3803-4708-9790-94c965927e2c] Luis Antonio Gracia Mazuca Ph.D. Research Associate Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu<http://utep.edu/>

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issue with ChimeraX 1.10 in snapdragon windows 11
by Erramilli, Satchal 24 Jul '25

24 Jul '25

Hello, I am reaching out to ask if there are any compatibility issues with ChimeraX 1.10 in Snapdragon Windows 11. The earlier version, 1.9, worked, but 1.10 doesn't. Is this a known issue with the Snapdragon architecture? Thanks, Satchal Erramilli ============================================================ This electronic message transmission and any attachments are confidential and/or proprietary and may constitute legally privileged information of Meso Scale Diagnostics, LLC. The information is intended for solely the use of "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu>. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance of this information is strictly prohibited. You are not authorized to retain it in any form nor to re-transmit it, and you should destroy this email immediately. If you have received this electronic transmission in error, please notify us by telephone (240-314-2600) or by electronic mail to the sender of this email, "Erramilli, Satchal" <SErramilli(a)meso-scale.com>, immediately. ===========================================================

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boltz latest version with ChimeraX1.10
by svle＠tiscali.it 24 Jul '25

24 Jul '25

Hi, it is possible to install the latest version ( 2.1.1 ) of boltz in ChimeraX 1.10 with the command boltz install? Thanks. Saverio

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Correlation Question
by Amin, M.A.A. 23 Jul '25

23 Jul '25

Hello, I'm trying to get the correlation between 2 maps. I used the command: measure correlation #2 in_map #1 I also saved the resampled map. Then, I wrote a very simple python code that calculates the correlation coefficient as following: def compute_correlation(map1, map2): threshold = np.percentile(map1.flatten(), 99) # top 1% value mask = (map1 >= threshold) #& (map2 != 0) values1 = map1[mask] values2 = map2[mask] corr = np.corrcoef(values1, values2)[0, 1] return corr Although it is considered masking as it is done in ChimeraX, I was never able to get the correlation value I got from ChimeraX. I got 0.1 from the python code and 0.68 in ChimeraX. Any suggestions? Thank you -- Muhamed Amin, Ph.D Assistant Professor of Physics University of Groningen, Groningen, Netherlands

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show only extra density
by maria l 23 Jul '25

23 Jul '25

Good Morning, I have a cryoEM map and a pdb, after fitting them i see an extra density i can´t explain with my model (pdb), is there an easy way, in chimera (old version), to show only that extra density? Thanks M

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Multiple alignment
by Marco Sette 23 Jul '25

23 Jul '25

Dear all, I have few pdb structure and I would like to build a multiple alignment of the sequences based on structural alignment. While in Chimera it was an easy task I'm find some problems with ChimeraX since it returns a series of pairwise alignments (structure A vs. B, A vs. C, A vs. D) rather than a multiple one (A vs. B vs. C. vs. D). Is it possible to do? Thanks Best Marco -- Dr Marco Sette, PhD Department of Chemical Sciences and Technology The University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: Addendum to Terms and Conditions - UCSF
by Francois-Xavier Campbell-Valois 23 Jul '25

23 Jul '25

Hello, I approve this agreement to use UCSF ChimeraX License. Best regards, François-Xavier Campbell-Valois, PhD Professeur agrégé | Associate Professor Université d’Ottawa | University of Ottawa Department of Chemistry and Biomolecular Sciences D’Iorio Hall 10 Marie-Curie Private Ottawa ON K1N 6N5 CANADA Office: DRO 403 Lab: MRN 214C https://fxcampbellvalois.org<https://fxcampbellvalois.org/> https://www.researchgate.net/profile/Francois_Xavier_Campbell-Valois https://ca.linkedin.com/in/fxcampbellvaloishostpathogen -- De : mscontracting Med School Contracting via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Date : mardi, 22 juillet 2025 à 16:17 À : chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Objet : [chimerax-users] Addendum to Terms and Conditions - UCSF Attention : courriel externe | external email Hello, I work for the Regents of the University of Minnesota and its Medical School. I am requesting signature on our standard supplier addendum to your UCSF ChimeraX License Agreement, both attached here. Please follow the instructions below: 1. If you are in agreement with the language on the addendum DO NOT SIGN. 2. Reply to this email that you are in agreement then I will send the addendum for signature via Adobe-Sign. 3. If you will not be the signatory please supply their email address. 4. Finally, a fully executed addendum will be returned. Please reach out with any questions or concerns. Thank you, Mequila Stevenson University of Minnesota Medical School Contracting Team Office Hours Zoom Link<https://umn-private.zoom.us/j/98326567540> Contract Routing Form<https://app.smartsheet.com/b/form/a4575a3938724cc68881868255b69dbb> Request Status Dashboard<https://app.smartsheet.com/dashboards/p7w62cJR57Qp3W9m56XhjX7w72xCcjr54hXvw…> (will need to request access)

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Intersurf and Surfnet in ChimeraX
by mlopez＠ibv.csic.es 23 Jul '25

23 Jul '25

Good afternoon, Does anyone know where are the Intersuf and the Surfnet options in ChimeraX?. Thanks a lot.

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