- ChimeraX-users - RBVI Mailing Lists

Announcing chimerax-emacs
by Zach Pearson 05 Jul '24

05 Jul '24

Hi ChimeraX Users, Over the holiday, I wrote a package that will let you use the command line from Emacs, leveraging ChimeraX’s rest server. https://github.com/zjp/chimerax-emacs This should be helpful if you use Emacs as your main editor and you want to debug your bundles without leaving your editors. Contributions from other emacs users welcome. — Zach

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Doubt about sequence visualization after real.space.refinement in phenix
by Leyre Marin Arraiza 04 Jul '24

04 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding model sequence visualization after real.space.refinement in phenix. After I worked on my model in ISOLDE and Coot, I deleted some residues that were out of the map density. Then, a dashed line appeared in my model, connecting the gap between the remaining residues (example, ALA97------GLN110). When I visualize the model sequence in ChimeraX, the deleted residues appear boxed with a rectangle, to indicate they are missing in the structure. Once I get the results back from the phenix real.space.refinement, and I visualize the model sequence in ChimeraX again, the deleted residues do not appear boxed anymore, but they are gone instead from the visualized sequence, keeping their corresponding numbers but not showing a boxed gap (in the example I mentioned they jump from 97 to 110 directly). I would like to keep the deleted residues boxed in the sequence when I visualize it. Is that possible? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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show 5% or 10% Z-axis of a fibril density
by Binh Nguyen 04 Jul '24

04 Jul '24

Dear all, Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map? [cid:11c579f0-867a-4136-b817-27e4c071e57e] I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. 1. Use volume eraser with a big diameter sphere 2. Build a rough backbone carbon model in 1 layer, and do zone selection. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Doubt about chimera
by DIEGO ANGOSTO BAZARRA 03 Jul '24

03 Jul '24

Hello, My name is Diego. I’m a beginner user of ChimeraX (1.8) and I was wondering if there is an option to check the % of similarity between two structures after making the matchmaker. I mean, I make a matchmaker with two structures, can I see the % of similarity between these two structures? Not between the sequences, but between the structures. Thank you very much for your time and attention. Best regards Dr. Diego Angosto Bazarra Molecular inflammation and experimental surgery group. IMIB. University Hospital Virgen de la Arrixaca

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ChimeraX workshop
by Jisoo Hwang 03 Jul '24

03 Jul '24

To whom it may concern, Good afternoon! I hope this email finds you well. I'm a student doing research at Johns Hopkins and was wondering if it'll be possible for us to set up a zoom meeting to ask some questions about the software. It's my first time using the software and it would be incredibly helpful if we can have a short workshop going over the features of ChimeraX. We're trying to include a 3D structure in a paper that we're planning on publishing soon. Please let me know if there's any other resource that you can point us to if we can't do a zoom meeting. Thank you so much for your help! Best, Suzie Hwang

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Request for Assistance: Selecting and Visualizing Interacting Residues in UCSF ChimeraX
by Rashmi Aggarwal 30 Jun '24

30 Jun '24

Dear UCSF ChimeraX Support Team, My name is Rashmi, and I am currently working on molecular docking studies as part of my research. I have been using UCSF ChimeraX version 1.8 for visualizing and analyzing protein structures. I am facing difficulties in performing the following tasks related to identifying interacting residues between chains A and B within 4 angstroms, similar to what I have previously done in PyMOL: 1. Select residues in chain A that are within 4 angstroms of chain B: select interactA, byres ((chain A) within 4 of (chain B)) 2. Select residues in chain B that are within 4 angstroms of chain A: select interactB, byres ((chain B) within 4 of (chain A)) 3. Combine the selections for interacting residues: select interaction_residues, interactA or interactB 4. Show interacting residues in stick representation and color them yellow: show sticks, interaction_residuescolor yellow, interaction_residues Despite attempting various commands and exploring the graphical user interface, I have been unable to achieve the desired results using UCSF ChimeraX. Could you please provide guidance on the correct commands or steps to accomplish this task in ChimeraX? Any assistance or advice would be greatly appreciated, as I have a pending deadline for my project. Thank you very much for your attention to this matter. I look forward to your prompt response. Best regards, Rashmi

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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 30 Jun '24

30 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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