June 2024 - ChimeraX-users - RBVI Mailing Lists

Aligning small molecules in Chimera
by Prathvi Singh 30 Jun '24

30 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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RMSD does not make sense in a few cases
by Roden Deng Luo 29 Jun '24

29 Jun '24

Hello ChimeraX Team, In the attached screenshot, #1 and #3 are almost overlapping, but get an RMSD as 57. I occasionally encounter this. The session and log files are attached. In short, to reproduce, open 5nl2.cif and emd_3658.map; fitmap #1 in #2 search 1000; rmsd #1 to #3. This happened rarely, but in this case, it happened twice. It might be that I fit other structures first. But I indeed click "Clear List" and "close session" after each fitting. The second top hit's RMSD seems to make sense in the attached session (screenshot attached too). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Where has the ribbon style editor gotten to?
by Dearborn, Altaira (NIH/NIAID) [E] 28 Jun '24

28 Jun '24

I tried the NIH3D presets to prepare my structure for 3D printing. The large size of the complex, however, makes those settings still too lacey for the NIH 3D printing service. I need to edit the ribbon sizes. The youtube tutorials from the NIH 3D Printing Exchange are 7-10 years old and their instructions to open the Ribbon Style Editor no longer match chimerax. Has this feature been renamed and moved? Thank you, Altaira Dearborn

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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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ChimeraX install problems
by Alexander Hung Lee 27 Jun '24

27 Jun '24

I tried to install ChimeraX daily build on a fresh install of Ubuntu 24. When I launch the program, the log says "Available bundle cache has not been initialized yet." Another oddity I"ve noted is that tying to run a python script w/ "chimerax --nogui --silent --offscreen --script path/to/script" works but "chimerax --script path/to/script" doesn't. I just get a black screen. There also isn't a stable build for Ubuntu 24, only daily builds. Should I downgrade my OS? Alex

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induce mutations in protein structure
by Mamadou Sangare 27 Jun '24

27 Jun '24

Dear, I'm new in chimera and I wouldlike to know how to induce mutations in protein structure, in other words, how to replace one residue by another in the protein structure. Kind regards! Mamadou SANGARE, PhD student ACE-B,Mali

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Feature suggestions for the Segmentations tool
by Ricardo Righetto 27 Jun '24

27 Jun '24

Hi, Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data! Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation: * Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI. Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more. Thank you and have a nice weekend! -- Ricardo Diogo Righetto

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Re: ChimeraX does not Support .stl files?
by Zach Pearson 26 Jun '24

26 Jun '24

Hi Kevin, Please direct questions about ChimeraX to our mailing list, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment. Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can. — Zach > On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney(a)uab.edu> wrote: > > Hello Dr. Pearson, > Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. > > Sincerely, > Kevin Maroney > M.S. Biotechnology > University of California, Irvine > PhD Student > University of Alabama at Birmingham

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transparency using in movie making
by Yanhe Zhao 26 Jun '24

26 Jun '24

Dear ChimeraX team, I have a map with model docking and am making movie. My plan is to fade away the map to show the docked model for next step. I tried the crossfade which works. But I want to use the transparency command for this purpose because I want to keep the map at specific transparency level, like 80%. The chimera has command like 'surftransparency 80 #1 50'. I was wondering what is the similar command in ChimeraX? Thanks and cheers, Yanhe

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Sequence based selections
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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