May 2024 - ChimeraX-users - RBVI Mailing Lists

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

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Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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abbreviation for transparentbackground please
by Anne-Frances Miller 13 Jan '25

13 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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color bfactor by alphafold palette
by Agnieszka Obarska 11 Nov '24

11 Nov '24

Hi, I’ve just would like to let you know that we’ve noticed recently that alphafold palette in ChimeraX is not consistent with original AlphaFold coloring. Please see the slide attached. On the left there is a model colored by the “color bfactor pal alpha” command in ChimeraX while on the right there is the same model colored according to AlphaFold coloring scheme. Best, Agnieszka

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NICE DCV graphics error
by georg.kempf＠fmi.ch 28 Jun '24

28 Jun '24

Dear ChimeraX developers and users, we would like to use ChimeraX in a virtual session using the “NICE DCV” software. We verified that OpenGL hardware rendering is working in the virtual session (glxinfo, glxgears, nvidia-smi) but when opening a structure in ChimeraX, we get the below error. We tried it with different versions of ChimeraX (1.8.dev202311220127, 1.6.1 stable) on Ubuntu 20.04.6 LTS. Since the error doesn’t appear when using ChimeraX on the physical display of the same workstation(s) (where the DCV server is running) it must be related to the virtual session context. I was wondering if anyone knows what could be the cause of the error and in which direction to look regarding debugging? This is the traceback from ChimeraX: 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 = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Traceback (most recent call last): File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 226, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 626, in _compute_shadowmaps multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1628, in use_multishadow_map self._start_rendering_multishadowmap(center, radius, size) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1711, in _start_rendering_multishadowmap fb = r.start_depth_render(self._multishadow_map_framebuffer, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1356, in start_depth_render if not fb.activate(): ^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2309, in activate fbo = self.framebuffer_id ^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2305, in framebuffer_id self._fbo = fbo = self._create_framebuffer() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2141, in _create_framebuffer fbo = self._create_fbo(self.color_texture or self._color_rb, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2169, in _create_fbo GL.glDrawBuffer(GL.GL_NONE) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Many thanks! Kind regards, Georg

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Bundles with dependencies
by Vincent Mallet 24 Jun '24

24 Jun '24

Hello, Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file. I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace... I am hoping you can help me, thanks in advance for the help ! Best, Vincent

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Rotation of the multi-model object using the symmetric axis
by Enrico Martinez 03 Jun '24

03 Jun '24

Dear Chimera-X users! I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried: # turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250 but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ? Many thanks in advance Enrico

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