- ChimeraX-users - RBVI Mailing Lists

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 11 Feb '26

11 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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expression
by Timothy Springer 09 Feb '26

09 Feb '26

Hi, the sidechains of residues 35 and 80 are contained within the selection. I am trying to remove the sidechains of residues 35 and 80 when saving a new name. what is wrong with this? name frozen conVup sel &~[:35,80&sideonly] name frozen conVup sel &~:[35,80]&sideonly I subsequently found I could solve it with ~select #1:35,80&sideonly name frozen conVup sel - 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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Worm representation of RMSD between two structures
by ruizarroyo＠ynamlab.org 07 Feb '26

07 Feb '26

Dear ChimeraX community, I am trying to make a figure to show the loop movement between two conformations of the same protein. For that, I would like to use a worm representation following these steps: -Trim residues so they all match in length between both models. -Matchmaker to align them -Calculate RMSD -... Next? From here, I would like to compute the RMSD value for each residue pair and use it to generate a worm representation; however, I cannot find any information about how to do this in ChimeraX. Is there any manual that I am missing? I appreciate any feedback that you may provide. Looking for your response. Best, Victor Ruiz

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Scenes
by Timothy Springer 05 Feb '26

05 Feb '26

Scenes has a bug with centroids in a .cxc file. When I omit the centroids, scenes works fine. 8 hydrogen bonds found define centroid #1/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01 Centroid 'centroid' placed at [216.18133333 173.87416667 191.88966667] close #3.1 distance #1.3 #1/V:38@NE2 color black dashes 6 radius 0.04 Distance between a4b1_12G10_VCAMD1D3_core_122_real_space_refined_123.pdb #!1/V GLN 38 NE2 and centroid #1.3: 3.474Å define centroid #2/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01 Centroid 'centroid' placed at [215.46366667 173.33033333 193.372 ] show :Mg color :Ca yellow style :Ca, Mg sphere Changed 12 atom styles size :CA, Mg atomRadius +0.5 Changed 12 atom radii color :Ca yellow color :Mg gray select clear windowsize 946 1210 view matrix camera 0.61619,-0.78632,0.04465,217.04,0.17445,0.080986,-0.98133,138.47,0.76803,0.61248,0.18708,205.73 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99998,0.0014978,0.0060567,-0.7471,-0.0012816,0.99937,-0.035532,7.7363,-0.0061061,0.035524,0.99935,-6.4316,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0 scenes save vcam_inter scenes restore vcam_inter Traceback (most recent call last): File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 816, in dropEvent _open_dropped_file(self.session, p) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 216, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 510, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 498, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 48, in open return open_command_script(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 171, in open_command_script _run_commands(session, commands, directory = dirname(path), log = log) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 184, in _run_commands run(session, cmd, log=log) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/cmd.py", line 61, in restore_scene session.scenes.restore_scene(scene_name) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/manager.py", line 102, in restore_scene self.get_scene(scene_name).restore_scene() File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/scene.py", line 198, in restore_scene model.restore_scene(scene_data) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 273, in restore_scene Model.restore_scene(self, scene_data['model state']) ~~~~~~~~~~^^^^^^^^^^^^^^^ KeyError: 'model state' KeyError: 'model state' File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 273, in restore_scene Model.restore_scene(self, scene_data['model state']) ~~~~~~~~~~^^^^^^^^^^^^^^^ - 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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ViewDock suggestions
by Andrii Kyrylchuk 04 Feb '26

04 Feb '26

Hi Chimera team! I’d like to raise two points about the new ViewDock window: 1. It would be great to have a count of displayed ligands shown somewhere in the window. For now there’s no easy way – I either count them manually, or export a |mol2| file and use |grep ... | wc -l|. 2. If I sort ligands by something else than Total Energy (which is how they are sorted in the |mol2| file), and then use arrow keys to navigate the list (either in the ViewDock or in the 3D window) the ligands are being shown in a chaotic order, which appears to be the original order from the |mol2| file. Is it possible to fix this behavior? Thank you for the great work! Sincerely, Andrii 

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