- Chimera-users - RBVI Mailing Lists

chimera display window issue
by Rechiche, Othman 09 Dec '25

09 Dec '25

Hi Chimera team, I’d like to bring to your attention an issue I’m encountering with the model display window (see attached images). As shown, the window appears incomplete. This problem started only after upgrading to the new macOS Tahoe—I did not experience it on macOS Sequoia. I’m currently using chimera-alpha-mac64.dmg (MD5: 555a52a5b12e1a617013213bf0f66c8d), the latest daily build. Could someone please take a look and advise on a possible solution? I would greatly appreciate your help. Thank you very much. Best regards, Othman ______________________________________ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.

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Write_DMS was not found
by 肖磊 09 Dec '25

09 Dec '25

Greetings, I can not find WRITE_DMS in ChimeraX. Is WRITE_DMS removed?

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CHIMERA X1.11 RELEASE - 12.01.25
by Laura Oliveira Gomes 01 Dec '25

01 Dec '25

Dear ChimeraX Support Team, I am writing to ask about the release of *ChimeraX version 1.11*, which is expected today. Is it already available for download? Since I need to use the software today, would you recommend waiting for the new release or downloading the previous version for now? Thank you, Laura Oliveira Gomes

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About present the result of DiffDock using Chimera
by galxj 18 Nov '25

18 Nov '25

Dear Sir/Madam, I am a user of the Chimera software. I have obtained some molecular docking results from DiffDock, where the ligand molecules are in SDF format and the receptor protein is in PDB format. May I ask if it's possible to view the docking results using Chimera? I have tried many times but keep encountering errors. I also attempted to convert the SDF file to PDB format and opened both files together. Although both molecules are displayed, it is clear that the docking has not been performed correctly. Best Regards, Alei Geng

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Chimera and ChimerX issues after update to MacOS Tahoe
by Rechiche, Othman 25 Sep '25

25 Sep '25

Hi everyone, I recently updated to MacOS Tahoe, Since then I encountered several issues with Chimera, ChmieraX and python. I installed and removed and reinstalled the apps but I still get the same error. For chimera I get this error: [Screenshot 2025-09-24 at 12.08.51 AM.png] FOr ChimeraX, when I try to open a session, it complains that the session was created with another version of python. I opened that session successfully several times before to the update of MacOS and I have never seen this error before. Failed opening file /Users/x/x/x/x/x/x/x/x.pyc: Python code was compiled for a different version of Python Can you please help me fix this? Best Regards, Othman Dr. Othman Rechiche Herbert Irving Comprehensive Cancer Center Columbia University Medical Center Columbia University New York, NY 10032 email: or2296(a)cumc.columbia.edu phone: +1 (814) 880-5554

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Mapping conservation onto a structure
by Shelley Copley 25 Sep '25

25 Sep '25

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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Announcement: Release of DOCK 6.13
by Scott Brozell 16 Jul '25

16 Jul '25

We are pleased to announce the release of DOCK 6.13. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.13 is available for download and free for academic users at https://dock.compbio.ucsf.edu/DOCK_6/index.htm This release includes new methods for de novo design: new biasing algorithms in DOCK_DN enable the prioritization of both fragments and torsions. Combined with parallel-based clustering and pruning algorithms that enable the efficient removal of duplicate molecules during growth, these approaches lead to ensembles with more drug-like characteristics. A number of incremental improvements are also available in this release notably for DOCK's genetic algorithm DOCK_GA and for Descriptor Score. For full information on what is new in DOCK 6.13, please visit: https://dock.compbio.ucsf.edu/DOCK_6/new_in_6.13.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. https://dock.compbio.ucsf.edu

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Composite map: select only voxels within a range of resolution?
by Samuel Leite Guimaraes 29 Jun '25

29 Jun '25

Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.

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Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 24 Jun '25

24 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

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Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 22 Jun '25

22 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

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