December 2024 - ChimeraX-users - RBVI Mailing Lists

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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get help with changing the cartoons ribbon to ball sticks
by Nhi Hoang 02 Jan '25

02 Jan '25

Hi. I am a sophomore at Le Quy Don High School in Danang City, Vietnam. I am using ChimeraX to display a model for my little project, and I have found a small trigger that I want to get help with. My problem is I cannot change the cartoon of selected residues from ribbons to ball sticks, after I have preset the model with cartoon ribbons. I wonder if this problem is due to the application and its limits or because of my device. I have attached an image presenting the coding and the model for a clear description of my problem. If possible, I am really willing to receive some advice from you in tackling this problem. Thank you very much. Best, Nhi Hoang. [image: image.png]

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Vector in ChimeraX
by Vitali James 31 Dec '24

31 Dec '24

Dear ChimeraX, Can you please help me to connect two pseudo-atoms by vector in ChimeraX. In the attached image (chimera.png), it was smoothly done in the past, but now the same file looks like a dotted line in chimeraX( e.g vector.PNG). Is it possible to control the color and style of this dotted vector line? best regards J. Vitali

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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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Unable to show interactions between bases and protein
by ADINDA 27 Dec '24

27 Dec '24

Dear Chimerax team, Hi, I am trying to find the interactions between my RNA and protein but have been unable to do so. I've been using the "contacts" function but it's not been working as expected. The command line that I gave was: contacts #1.2 restrict #1.1 makePseudobonds true reveal true log true where #1.2 is my RNA and #1.1 is my protein. Even when I switch the positions of #1.2 and #1.1, it still doesn't work (0 contacts shown). Do you have any tips on how I can rectify this? Happy holidays! Best regards, Adinda

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How probe radius should affect exposed surface area?
by Alon BenDavid 25 Dec '24

25 Dec '24

Hi, I am trying to measure the exposed surface area of lysine residues in DNaseI (4AWN). I am using the "measure sasa" command. To my surprise, when I am increasing the probe radius (1.4 A, 5 A, 10 A etc.) I receive larger exposed surface area. Is that OK? Many thanks, Alon

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"straightening" or stretching disordered residues from alphafold models
by Daniel Elnatan 20 Dec '24

20 Dec '24

Hi folks, I’ve been playing around with AlphaFold to get protein structures and visualizing them in ChimeraX. For some proteins with a lots of disordered regions (e.g. between non-interacting, well-folded domains), the ‘noodles’ end up being a visual clutter. So I wrote a custom python function to be used in ChimeraX that would ‘straighten’ or stretch selected residues (typically the disordered or low pLDDT regions) by simply assigning torsion angles for a more ‘straight’ structure. I do this via the `Residue.set_phi()` and `Residue.set_psi()` methods. Here’s a link to my Python script: https://github.com/delnatan/colabfold_chunker_utils/blob/65f2419425de300df5… The command is run simply with `straighten #1:13-20`. Now when there are multiple chains within the same model, altering the torsion angles may actually move the relative positioning between the chains. Is there an easy way to avoid this? perhaps by passing an extra argument as ‘reference’ so one can place the structure back to its original coordinate for the reference residues. I’m not too familiar with the programming API just yet, but what is the correct way to do this? Maybe that the reference coordinates can be saved before assigning the torsion angles, and a transformation matrix can be computed only for the reference region between the original and moved structure. The altered chain can then be moved back by applying this transformation matrix? Thanks! -Daniel

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Help with ChimeraX modeling
by Christman, Nick 18 Dec '24

18 Dec '24

Hello, I am a graduate student at Indiana University, and I am trying to use ChimeraX to visualize positively charged surface accessible residues on some protein models. I've been trying to find the right combination of commands to get this to work but haven't been successful. I know how to calculate surface accessible residues, how to color the surface accessibility of residues within a selection on my model, and even how to calculate hydrophobicity of residues (related to charge), but I cannot figure out how to model the charge of surface exposed residues. Could you please point me in the right direction so I can get the models that I would like? Thanks! Nick Christman (He/Him) Dalia Lab Indiana University

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poc file of castp not support
by Prem Dorjee Tamang 17 Dec '24

17 Dec '24

sir/madam this chimer_x version 1.8 and 1.9 both the tools not support the poc file just look in thes matter

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initial dark mode support
by Greg Couch 17 Dec '24

17 Dec '24

FYI, the ChimeraX daily build now has dark mode support. So if you set your desktop to use dark mode, ChimeraX should follow. It's a work in progress, and it depends on developer's making their code dark mode aware (eg., icons may need to be modified), but if you notice any black text on a dark background, please let me know. -- Greg

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