February 2026 - ChimeraX-users - RBVI Mailing Lists

how to align models to 0,0,0 z axis for saving to PDB ?
by Mitch Murphy 24 Feb '26

24 Feb '26

please help i cant figure out how to align a complicated set of models so the barrell of my hexameric ion channel is aligned along z axis and centered at 0,0,0 to save a pdb close cd /Users/mitch/github/hmx/jahani/egfrv3 log clear # ---------------- tmCLIC1 ---------------- open ../charmmgui-clic1/step1_pdbreader.pdb id 99 center 0,0,0 color :1-23 blue color :24-58 green color :59-241 red torsion :25@c:26@n,ca,c -60; torsion :26@n,ca,c:27@n -45 torsion :26@c:27@n,ca,c -60; torsion :27@n,ca,c:28@n -45 torsion :27@c:28@n,ca,c -60; torsion :28@n,ca,c:29@n -45 torsion :28@c:29@n,ca,c -60; torsion :29@n,ca,c:30@n -45 torsion :29@c:30@n,ca,c -60; torsion :30@n,ca,c:31@n -45 torsion :30@c:31@n,ca,c -60; torsion :31@n,ca,c:32@n -45 torsion :31@c:32@n,ca,c -60; torsion :32@n,ca,c:33@n -45 torsion :32@c:33@n,ca,c -60; torsion :33@n,ca,c:34@n -45 torsion :33@c:34@n,ca,c -60; torsion :34@n,ca,c:35@n -45 torsion :34@c:35@n,ca,c -60; torsion :35@n,ca,c:36@n -45 torsion :35@c:36@n,ca,c -60; torsion :36@n,ca,c:37@n -45 torsion :36@c:37@n,ca,c -60; torsion :37@n,ca,c:38@n -45 torsion :37@c:38@n,ca,c -60; torsion :38@n,ca,c:39@n -45 torsion :38@c:39@n,ca,c -60; torsion :39@n,ca,c:40@n -45 torsion :39@c:40@n,ca,c -60; torsion :40@n,ca,c:41@n -45 torsion :40@c:41@n,ca,c -60; torsion :41@n,ca,c:42@n -45 torsion :41@c:42@n,ca,c -60; torsion :42@n,ca,c:43@n -45 torsion :42@c:43@n,ca,c -60; torsion :43@n,ca,c:44@n -45 torsion :43@c:44@n,ca,c -60; torsion :44@n,ca,c:45@n -45 torsion :44@c:45@n,ca,c -60; torsion :45@n,ca,c:46@n -45 torsion :45@c:46@n,ca,c -60; torsion :46@n,ca,c:47@n -45 torsion :46@c:47@n,ca,c -60; torsion :47@n,ca,c:48@n -45 torsion :47@c:48@n,ca,c -60; torsion :48@n,ca,c:49@n -45 torsion :48@c:49@n,ca,c -60; torsion :49@n,ca,c:50@n -45 torsion :49@c:50@n,ca,c -60; torsion :50@n,ca,c:51@n -45 torsion :50@c:51@n,ca,c -60; torsion :51@n,ca,c:52@n -45 torsion :51@c:52@n,ca,c -60; torsion :52@n,ca,c:53@n -45 torsion :52@c:53@n,ca,c -60; torsion :53@n,ca,c:54@n -45 torsion :53@c:54@n,ca,c -60; torsion :54@n,ca,c:55@n -45 torsion :54@c:55@n,ca,c -60; torsion :55@n,ca,c:56@n -45 torsion :55@c:56@n,ca,c -60; torsion :56@n,ca,c:57@n -45 torsion :56@c:57@n,ca,c -60; torsion :57@n,ca,c:58@n -45 torsion :57@c:58@n,ca,c -60; torsion :58@n,ca,c:59@n -45 torsion :22@c:23@n,ca,c 60 sym #99 C6 center :17 axis :24,58@ca newModel true setattr #1.1 chains chain_id A create true setattr #1.2 chains chain_id B create true setattr #1.3 chains chain_id C create true setattr #1.4 chains chain_id D create true setattr #1.5 chains chain_id E create true setattr #1.6 chains chain_id F create true delete #99 rename #1 tmCLIC1 rename #1.1 tmCLIC1-A rename #1.2 tmCLIC1-B rename #1.3 tmCLIC1-C rename #1.4 tmCLIC1-D rename #1.5 tmCLIC1-E rename #1.6 tmCLIC1-F # ---------------- EGFRv3 ---------------- #runscript egfrv3_v1.cxc # ---------------- OSMR ---------------- open Q99650 fromDatabase alphafold version 6 id 3.1 center 0,0,0 torsion #3.1:804@c:805@n,ca,c 60; torsion #3.1:805@n,ca,c:806@n 45 torsion #3.1:805@c:806@n,ca,c -120; torsion #3.1:806@n,ca,c:807@n 130 torsion #3.1:806@c:807@n,ca,c -120; torsion #3.1:807@n,ca,c:808@n 130 torsion #3.1:807@c:808@n,ca,c -120; torsion #3.1:808@n,ca,c:809@n 130 torsion #3.1:808@c:809@n,ca,c -120; torsion #3.1:809@n,ca,c:810@n 130 delete #3.1:836-979 rename #3 OSMR rename #3.1 OSMR-I combine #3.1 modelid 3.2 name OSMR-J setattr #3.1 chains chain_id I create true setattr #3.2 chains chain_id J create true turn x 270 models #3 turn z 180 models #3.1 move y 90 models #3 move x 200 models #3.1 move x -200 models #3.2 # ---------------- DISPLAY ---------------- delete ~protein rainbow #1-3 structures palette Paired-12 surface #1-3 transparency 0.5 move x 5.08443251 models #1 move y -47.21837099 models #1 move z -14.00102839 models #1 #turn x -67.233 models #1 center 0,0,0 #turn y -31.805 models #1 center 0,0,0 #turn z -69.036 models #1 center 0,0,0 define axis #1 primary false tertiary true radius 1 padding 100 id 4.1 define axis frompoint -300,0,0 topoint 300,0,0 color red id 4.2 define axis frompoint 0,-300,0 topoint 0,300,0 color green id 4.3 define axis frompoint 0,0,-300 topoint 0,0,300 color blue id 4.4 view position #1 sameAsModels #4.4 angle #4.1 #4.2 angle #4.1 #4.3 angle #4.1 #4.4

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New ChimeraX Plugin: Cube'n Tube
by Cairoli Tamino 24 Feb '26

24 Feb '26

Hey all, I’m happy to share a small plugin I recently developed for UCSF ChimeraX: Cube’n Tube. It extends the standard eraser sphere tool. Instead of only a sphere, you can now erase with cubes, cylinders (frustum), cones, or even define your own custom shape. While working with various protein structures, I often felt that a spherical eraser is not always ideal. Especially when trying to remove part of a filament, micelle density, or isolate one asymmetric unit of a larger assembly. I was really missing a more dynamic eraser tool, so I decided to build it. I also implemented a simple undo/redo function for the eraser tool. I cannot count how often I misclicked and had to restart my masking from zero… Now there is a one-step undo (limited to one step to keep it smooth on all machines). The custom shape option works particularly well together with a fitted atomic model (for example from AlphaFold) to erase everything outside the region of interest. Cube’n Tube can be downloaded directly from the ChimeraX Tool Shed or from GitHub (https://github.com/TaminoCairoli/CubeNTube) If you are missing a feature or have ideas for improvements, feel free to open an issue on GitHub. Many thanks to the team (especially Tom Goddard) at University of California, San Francisco for building such a powerful and well-documented tool, and thanks to Pavel Afanasyev, Julius Rabl and Dianhong Wang for discussion and testing. Best, Tamino

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Trouble with ISOLDE installation.
by Michel THEPAUT 23 Feb '26

23 Feb '26

Dear help team, I try to install ISOLDE from ChimeraX, using Tool / More Tools... menu: Clicking on Install looks to work, because I have the information below which appears un Log of ChimeraX But it looks like nothing happens as progression bar (red arrow above) do not progress, even after more than half an hour. I am using ChimeraX installed thanks to SBGrid: Is there a known problem or an other way to do this installation ? Thank you for your help. Best regards. -- Michel Thépaut Institut de Biologie Structurale MIT/M&P CAMPUS EPN 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9

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Improvements to ChimeraX 1.11.1
by Anindya Karmaker 20 Feb '26

20 Feb '26

Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you. Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker(a)ucdavis.edu <akarmaker(a)ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>

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Helpful cheat sheet for ChimeraX
by Alejandro Daniel Pereira 19 Feb '26

19 Feb '26

Hi ChimeraX team, My name is Alejandro Pereira, and I am a PhD candidate in the Trent Lab with the Department of Microbiology at the University of Georgia. I recently created a ChimeraX cheat sheet that highlights a range of useful features and includes publication‑quality examples. As a developing scientist, effective science communication is extremely important to me. With that in mind, I wanted to ask whether the ChimeraX team might be interested in including this cheat sheet on your documentation page or website. My goal is to provide beginners with a clear, accessible resource that introduces core concepts and showcases key features without the potential confusion of navigating extensive documentation. If this is something you’re interested in, please let me know, and I’d be happy to send it over. I only ask that proper citation be included to ensure appropriate credit. I’d also be glad to adapt the material to meet any formatting or style preferences you may have. Best, Alejandro Pereira Microbiology Department Trent Lab Ph.D. Candidate e: Alejandro.Pereira(a)uga.edu<mailto:Alejandro.pereira@uga.edu> [University of Georgia]

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Reading Coarse Grained Trajectories into UCSF ChimeraX
by Wijeratne, Arambewela A 12 Feb '26

12 Feb '26

Hello, I have a quick question regarding loading of coarse-grained molecular simulation trajectories generated using the HPS force-field . I have a PSF and DCD generated out of 2 systems, one that contains only protein beads and another of both protein and DNA. I find that the protein only system is read by UCSF ChimeraX and reads both the PSF and DCD of that system, while the protein and DNA system doesn't. I get this error: IndexError: Cannot create Element with atomic number 119 File "atomic_cpp/cymol.pyx", line 967, in chimerax.atomic.cymol.Element._int_to_cpp_element See log for complete Python traceback. I do want to emphasize that since the HPS model is a single bead coarse-grained model, the actual mass of the nucleic acid beads encompass the mass of the sugar and nucleobase and might not reflect any 'elemental mass', (that is what I understood of the error anyway as there were residues which are having greater mass than recorded elements.) However, despite the protein beads also having masses of entire amino acid residues, not elements, the protein only simulation rendered fine. I was wondering whether there is a work around for this? To prevent ChimeraX from seeking element/atom and just utilizing the PSF file and then reading the DCD file as is? Thank you for your time, Best, Sunera

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ArtiaX memory issue
by Bullitt, Esther 11 Feb '26

11 Feb '26

hi, I am able to open a tomogram in ChimeraX, but when I launch ArtiaX and try to open the same tomogram: 1440, 1023, 512, I get the error below. Is there somewhere I can increase the memory it is allowed to use? How much does it need? thank you for any assistance. Sincerely, Esther An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ) ) Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259, in _draw_scene draw_opaque(r, opaque_drawings) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1572, in _draw_multiple d.draw(renderer, draw_pass) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 936, in draw drawing = self._update_view_axis(renderer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 662, in _update_view_axis pd = self._update_3d_texture_planes(view_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 714, in _update_3d_texture_planes pd = self._texture_3d_planes() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 724, in _texture_3d_planes pd = Texture3dPlanes(self) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1551, in __init__ self._fill_textures() File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1668, in _fill_textures t.reload_texture(td, now=True) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3210, in reload_texture self.fill_opengl_texture() File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3220, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3100, in initialize_texture GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2], File "src/latebind.pyx", line 40, in OpenGL_accelerate.latebind.LateBind.__call__ File "src/wrapper.pyx", line 319, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "src/wrapper.pyx", line 312, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ) )

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ChimeraX dowloading problem
by JORGE Y GARAY-COLON 11 Feb '26

11 Feb '26

Greetings, I am trying to download ChimeraX in my windows laptop but an error message appears (attached below) right after accepting the terms and conditions. I am selecting the ChimeraX-1.11.1.exe version. "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log."

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error message running fodseek
by Miller, David M 10 Feb '26

10 Feb '26

Hi, Foldseek ran successfully with PDB but crashed in an independent comparison to AlphaFold DB (see attached). Looks like a problem with alphafold file name? Thanks for your help. Best, david David M. Miller, III, PhD Professor Cell and Developmental Biology 465 21st Avenue South PMB 407935 3120 MRB III Vanderbilt University Nashville, TN 37240-7935 (615) 343-3447 https://medschool.vanderbilt.edu/miller-lab/

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(no subject)
by Timothy Springer 09 Feb '26

09 Feb '26

This works for Ca and Mg but not Mn size :CA, Mg,Mn atomRadius +0.5 - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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