December 2024 - ChimeraX-users - RBVI Mailing Lists

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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cartoon style setting
by junjie han 23 Dec '24

23 Dec '24

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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"straightening" or stretching disordered residues from alphafold models
by Daniel Elnatan 19 Dec '24

19 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 16 Dec '24

16 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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Re: [chimerax-announce] ChimeraX version 1.9 has been released
by Elaine Meng 16 Dec '24

16 Dec '24

Hi Dietmar, Thanks for your comments. Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing. You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html> Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck(a)uni-konstanz.de> wrote: > > Dear Elaine, dear ChimeraX developer Team, > > thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-) > > I have two requests/suggestions how your could improve ChimeraX further: > > a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it). > > b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem. > > All the best, > > Dietma > > Dietmar Funck > Biopolymer Chemistry > Chemistry Department > University of Konstanz

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ChimeraX version 1.9 has been released
by Elaine Meng 13 Dec '24

13 Dec '24

UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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embed ChimeraX into web pages
by Marius Mihasan 12 Dec '24

12 Dec '24

Hi I have been using ChimeraX for some time to generate .stl files and print various molecules and molecular scenes. I planning/working on making the pdb to stl file conversion semi-automatic and more user friendly by offering the users some predefined 3D-printable renderings of the molecule of their choice as well as some simple push-buttons that would allow them to do some very simple customisation in the renderings. Everything needs to be packaged in a simple to acces web-page that can be used by educators and students . In a way similar to how NIHPresets work, but in a webpage. Or how NIH 3D QuickSubmit works, but more interactive. Is there a way to embed ChimeraX into web pages as it can be done with, for example, with JSmol (Jmol)? If yes, could someone please point me in the right direction? Thanks --------- Marius Mihasan, PhD. Habil. Professor, BioActive Research Group Biochemistry and Molecular Biology Laboratory, Faculty of Biology Alexandru Ioan Cuza University of Iasi Room B228, Carol I Blvd, no 20A, Iasi, Romania, 700506 Tel: +40(0)232202434 Fax: +40(0)232201472 http://cercetare.bio.uaic.ro/cadre/pagini-personale/marius.mihasan/index.ht… Associate Professor Darie Biochemistry & Proteomics Group Department of Chemistry & Biomolecular Science Clarkson University Potsdam, NY 13699-5810, USA mmihasan(a)clarkson.edu

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