- ChimeraX-users - RBVI Mailing Lists

DNA/RNA style in ChimeraX
by Woo-Ri Shin 06 Feb '24

06 Feb '24

Hi I have a question about making images for protein-DNA(or RNA) complex structures. I want to make the round shape of DNA (or RNA) backbone using "nucrib" command which is provided on the web ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html) But this command doesn't work. I have the docking structure including RNA of chain A and protein of chain B. So then I modified the command like this: *alias nucrib cartoon style /A xsect oval width 1.6 thick 1.6* This command doesn't work and still initial cartoon style. Could you check this problem? [image: image.png] Thank you Best, Woo-Ri Shin -- *Woo-Ri Shin, Ph.D.* Department of Bioengineering University of Pennsylvania E-mail: wr1203(a)seas.upenn.edu Phone: +1 (267)213-2572 ᐧ

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Coloring maps based on segmentation
by M. Elizabeth Stroupe 05 Feb '24

05 Feb '24

Hi, I am having some trouble coloring my map based on segmentation. It used to be straightforward from the “Regions” menu of the segmentation tool, but now I am getting an error "TypeError: unsupported operand type(s) for *: 'float' and 'NoneType' File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/segger/regions.py", line 1884, in color_surface_pieces xyz = v - offset*n” I also tried to do it by line command but I confess I am not sure what to put for “seg-map”. Thank you for your help, Beth

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Information storage
by Cygler, Miroslaw 05 Feb '24

05 Feb '24

Hi, When ChimeraX opens, it restores list of commands used in previous session(s) and the files/sessions there were accessed previously (history). Where is this data stored on the computer? How can I preload specific settings to take effect on ChimeraX opening? Thanks, Mirek

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ChimeraX on new Apple cpus
by Enrico Martinez 05 Feb '24

05 Feb '24

Dear ChimeraX users! I am considering purchasing one of the recent macbook pro equipped with the modern M2 or M3 apple chips. Assuming that presently I am using the 2015 model equipped with the i7 4 core cpu and discrete radeon gpu, what should be expected increase of the performance in the case of recording of MD movies with ChimeraX using the performance of a new mac ?? Many thanks in advance Enrico

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Save PDB relative to map - does not store relative postion
by Dennis Dannecker 02 Feb '24

02 Feb '24

Hello, I am running into an issue with saving pdb coordinates and their relative postioning. I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool. However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship. I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information. Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model? Thank you for your help. Best regards, Dennis --------------------------------------------- Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

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Display volume default threshold level
by Chenwei Zhang 02 Feb '24

02 Feb '24

Dear UCSF ChimeraX developers, I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: _Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32_ May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help. Thank you in advance and look forward to your reply. Best, Chenwei

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Using GPU in chimerax
by Sharif, Omar 01 Feb '24

01 Feb '24

Hello, I am using Chimerax with a tool called DeepSSETracer, a model that performs segmentation on the secondary structure of 3d cryo density maps. I need GPUs and CUDA enabled to test the tool. When I run the model, I have a message in the log that says Cuda is not available although I am running on a machine where relevant Nvidia GPU drivers and Cuda are already installed and working properly. I am attaching the screenshot [cid:d821ceae-9b2c-4a88-a7ba-c45b2935bee2] Is there any way to enable GPU usage within the ChimeraX? Is there any way to check if ChimeraX is using GPU and CUDA? I will be waiting for your reply. Thanks in advance, Omar Omar Sharif Ph.D. student Department of Computer Science Old Dominion University Email: osharif(a)cs.odu.edu https://odu.zoom.us/my/omarsharif786

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Center atom
by Cygler, Miroslaw 31 Jan '24

31 Jan '24

Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek

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opening the session made with the new ChimeraX version using old ChimeraX
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I made a session (cxs) in the newest ChimeraX. It contains the models only. How can I open it in the older ChimeraX version? Maybe I can save the session in a different format to be able to open with the older version? Unfortunately, I cannot update the older version on one PC. Thank you. Kind regards, Dmitry

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transparency around the model only
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I have a cryo-EM 3D map and model. A model is fitted for only part of my cryo-EM map. Is there a command to make the map transparent only where the model is fitted in? Thank you. Kind regards, Dmitry

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Antivirus software warns about "Trojan.Win32.Diple" in 1.7.1 ChimeraX executable
by thomas.coudrat＠gmail.com 31 Jan '24

31 Jan '24

Hi ChimeraX list, When trying to install ChimeraX 1.7.1 Windows (md5: c79878497cfa2c1e0944e732ea4adc21) I get a warning from my antivirus software. See the description here: https://www.virustotal.com/gui/file/cc9b4af4e1a04fc647d082e04f60c111c7aeed1… In case the link doesn't work, it says that "Ikarus" is warning about "Trojan.Win32.Diple", while passing the checks with several other antivirus software. (I've seen a similar thread in the archive but it was from last year, therefore this one might be different) Kind regards, Thomas

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rrdistmaps in chimerax?
by Francisco Murphy Pérez 30 Jan '24

30 Jan '24

I just learned about this program called RRDistMaps https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410660/ in UCSF chimera. Is there something similar in chimeraX? Thanks

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Modeller using more than 1 template in Chimera Modeller
by Vladimir Saudek 29 Jan '24

29 Jan '24

Hello, Is it possible to model 3D structure within Chimera using several complementary pdb templates at once? This is possible in the stand alone Modeller but I was unable to find a tutorial/manual instruction how to do it in Chimera. Thank you Vladimir

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mixed backbone/sidechain display for N-terminal residue
by hirbond＠utexas.edu 28 Jan '24

28 Jan '24

Hi everyone, I've been working on a protein display that I want to explicitly show the sidechain and backbone atoms of the N terminal residue. The problem is with the cartoon representation. For the N terminal, the cartoon rep goes beyond the CA atom and sticks out. Any tip on how I can change it? I thought of eliminating the pseudobond representation for the CA atom so that the cartoon representation doesn't happen between C and CA but it did not work for me. Thanks!

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Problem with Chimerax on Ubuntu 20.04
by svle＠tiscali.it 26 Jan '24

26 Jan '24

Hi, I've installed Chimerax 1.7.1 using the .deb. When launching the application from the icon It appears the Chimerax window along with another error panel and after one or two seconds these are closed. If I call Chimerax from a shell I receive the following: $ chimerax NOTE: available bundle cache has not been initialized yet [48347:48390:0126/183239.131894:ERROR:skia_output_surface_impl.cc(927)] surface_size=1224x615 format=6 color_type=4 backend_format.isValid()=0 backend_format.backend()=5 backend_format.asGLFormat()=0 backend_format.asVkFormat()=0 backend_format.asVkFormat() vk_format=0 surface_origin=1 willGlFBO0=0 Segmentation fault (core dumped) If this can be useful on my laptop: $ uname -a Linux xxxx-Lenovo-IdeaPad-S340-15API 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux $ glxinfo -B name of display: :0 display: :0 screen: 0 direct rendering: Yes Extended renderer info (GLX_MESA_query_renderer): Vendor: AMD (0x1002) Device: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) (0x15d8) Version: 20.3.4 Accelerated: yes Video memory: 2048MB Unified memory: no Preferred profile: core (0x1) Max core profile version: 4.6 Max compat profile version: 4.6 Max GLES1 profile version: 1.1 Max GLES[23] profile version: 3.2 Memory info (GL_ATI_meminfo): VBO free memory - total: 866 MB, largest block: 866 MB VBO free aux. memory - total: 5689 MB, largest block: 5689 MB Texture free memory - total: 866 MB, largest block: 866 MB Texture free aux. memory - total: 5689 MB, largest block: 5689 MB Renderbuffer free memory - total: 866 MB, largest block: 866 MB Renderbuffer free aux. memory - total: 5689 MB, largest block: 5689 MB Memory info (GL_NVX_gpu_memory_info): Dedicated video memory: 2048 MB Total available memory: 7928 MB Currently available dedicated video memory: 866 MB OpenGL vendor string: AMD OpenGL renderer string: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) OpenGL core profile version string: 4.6 (Core Profile) Mesa 20.3.4 OpenGL core profile shading language version string: 4.60 OpenGL core profile context flags: (none) OpenGL core profile profile mask: core profile OpenGL version string: 4.6 (Compatibility Profile) Mesa 20.3.4 OpenGL shading language version string: 4.60 OpenGL context flags: (none) OpenGL profile mask: compatibility profile OpenGL ES profile version string: OpenGL ES 3.2 Mesa 20.3.4 OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20 The same problem also with Chimerax 1.7.0 but not 1.6. Thanks. Saverio

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CA atoms connected by tether when trying to show sidechains only in a model
by Samuel Haysom 25 Jan '24

25 Jan '24

Hello, I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. "show #1 & sidechain") the CA atoms become linked by tethers. [cid:image001.png@01DA4F98.8C977390] How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn't seem to apply here as I'm not showing the cartoon at all in the models where the CA tethers are present. KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Inquiry on Commercial Licensing for ChimeraX Plugin Development
by Jacky Chen 24 Jan '24

24 Jan '24

Dear Team ChimeraX, My name is Jacky Chen, and I am the sales representative at Oomii. Recently, we initiated a project aimed at developing an innovative ChimeraX plugin, specifically designed to enable interactive augmented reality features. To this end, Oomii has acquired two commercial licenses of ChimeraX in January 2024. As we progress, our intention is to offer the developed bundle for commercial sale to other users. However, upon reviewing the documentation available at: https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html, we noticed that it does not specify the licensing particulars for a bundle that utilizes both the ChimeraX API and proprietary code developed by Oomii. We are keen to ensure that our operations align with ChimeraX's licensing policies. Could you please provide guidance on the business rules that apply to the commercial distribution of such plugins? Additionally, if available, could you direct us to any precedent or contact information for companies that have navigated similar pathways? Your assistance in this matter is invaluable to us, and we eagerly await your insights. Thank you very much for your time and support. Warm regards, *Jacky Chen 陳志傑* *Sales Representative* * <https://oomii.com/>* *jackychen(a)oomii.com <jackychen(a)oomii.com>* *2F.-1, No.94, Baozhong Rd. Xindian Dist., New Taipei City, Taiwan 23144* *+886-2-8911-2347* <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> 乾淨無病毒。www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Feature question: "Worms" plots in "Render By Attribute"
by James Lingford 24 Jan '24

24 Jan '24

Dear ChimeraX team, I was wondering if ChimeraX v1.7+ has the function for rendering attributes by "Worms"? For example, rendering B-factors by the thickness of the backbone. I noticed that it's possible in legacy version of Chimera, which I have since installed and generated worm plots with: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedpecworm.html Is this doable in the latest ChimeraX versions, however? Many thanks for any help you can provide, James -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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Re: [Chimera-users] Chimera X menu "View" vs. "Focus"
by Eric Pettersen 23 Jan '24

23 Jan '24

Hi Christian, We named it “View” instead of “Focus” because it issues a “view” command, but your points have merit — “Focus” is more evocative of what the action actually does, and is less confusable with hide/show, so after some discussion we have renamed the menu item to “Focus” and the change will be in the next daily build. The menu item item still issues/logs a “view” command to do its work. We are aware that the direct equivalent of the “Fetch By ID” dialog is missing in ChimeraX and we intend to add it. It’s just a matter of implementation priorities, so it could still be a little while — but it’s useful to know that it’s definitely missed, which will make it more likely to get worked on sooner. Also, there is a list specifically for ChimeraX user issues — chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>, (cc’ed here), which would be better to discuss ChimeraX topics on than chimera-users… --Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 25, 2023, at 12:47 AM, C. Klein via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team > > first of all, thank you very much for your important and good work on the Chimera software. > > Two comments: > > I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. > > The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. > > Thank you and best wishes > Christian Klein > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Does ChimeraX work with tkinter?
by thlin＠oomii.com 22 Jan '24

22 Jan '24

I tried to use `tkinter` instead of `PyQt` but it does not work with ChimeraX 1.6 or 1.7's Python interpreter and the error message is shown below: ``` import _tkinter # If this fails your Python may not be configured for Tk ModuleNotFoundError: No module named '_tkinter' ``` One solution I've found was to `sudo apt install tk-dev` but it was required to`configure` and `make` ChimeraX's Python interpreter after. Does ChimeraX work with tkinter? If yes, then how to?

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Missing comand bar to open proteins
by Marina Contel 22 Jan '24

22 Jan '24

Hello, A few days ago, I was using ChimeraX and the command bar to open proteins disappeared. I have tried everything including uninstalling it and installing it again, and I have no clue how to solve it. I was wondering if you could give me some guidelines to get it back. That will be amazing because I need to start working with it as soon as possible because I have an assignment to hand this week. Thanks in advance! Kind regards, Marina

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[Inquire about the protein protein interaction results using chimeraX]
by ‍정혜연[학생](생명과학대학 유전생명공 학과) 22 Jan '24

22 Jan '24

Hi, I'm HyeYeon from KyungHee University. I am sending you an email because I have some questions while using ChimeraX. When I investigated the interaction between the two proteins using chimeraX, the results of the two runs were different even though they had the same sequence. One is the result from June of last year and the other is from January of this year. Did the PPI results change despite the same sequence as a result of the program update? I would appreciate it if you could check and reply. Thank you.

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Defining a variable that represents the number of models
by kkssy141＠gmail.com 20 Jan '24

20 Jan '24

Hello, Would it be possible to define a variable that represents the number of models? I want to make a chimerax script that aligns #1-#(N-1) to #N. For instance, if I have a script like this where N represents the number of models opened in ChimeraX and save it as test.cxc mm #1-#(N-1) to #N In bash, I can open my PDB files that are aligned to a crystal structure 1be9: chimerax *.pdb 1be9 test.cxc The number of models (N) will be a dynamic variable depending on how many PDB files I have. Thank you. Best, Siyoung ------------------ While writing, I figured the below would work. test.cxc: mm ~#1 to #1 In bash: chimerax 1be9 *.pdb test.cxc But I still want to ask this question to know whether it is possible to retrieve the number of models opened and set this to a variable in ChimeraX. Thanks.

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Option to convert shape to map?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi, Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)? This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc). I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have. Cheers Oli

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