- ChimeraX-users - RBVI Mailing Lists

Volume eraser as cube?
by Oliver Clarke 09 Jan '25

09 Jan '25

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

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Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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Assistance/guidance with ChimeraX
by Mahesh Chandrasekharan 03 Jan '25

03 Jan '25

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package! It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX? 2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer? Thank you, Best, Mahesh Mahesh B. Chandrasekharan, PhD Assistant Professor of Radiation Oncology Investigator, Huntsman Cancer Institute Adjunct Assistant Professor of Hematology & Hematological Malignancies University of Utah School of Medicine 2000 Circle of Hope Room 3715 Huntsman Cancer Institute Salt Lake City, UT 84112-5540 Phone: 801-213-4220 Administrative Assistant: Coreen Rankin (801-585-3599) Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

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Getting average of PAE values for a given region / interaction
by David S. Fay 02 Jan '25

02 Jan '25

Greetings and Happy New Year to All! My question is about broadly protein-protein interactions (PPIs. Last year several manuscripts came out proposing new metrics for assessing PPIs. This was in logical response to the growing understanding that ipTM (alone) is a fairly flawed metric, particularly for detecting interactions that involve a small number/fraction of the total residues. For those interested, I’ve pasted links to three such papers below (Coincidentally one is from a former roommate's lab, which I didn’t notice until recently!). Some may be easier to use than others (have GUIs). Tom Goddard and I emailed back and forth a bit about the relative merits of some of these metrics - nothing is perfect obviously (thank you again Tom). With respect to ChimeraX, I was wondering if there was a way to extract average PAE values after employing a cutoff. For example, "alphafold contacts /A distance 5 maxPae 5” will tell me that are "54 residue or atom pairs within distance 5 with pae <= 5”. But what if I want to know the average of those 54? Along those lines, for some PPIs there may be several spatially separated interfaces, with each one contributing to the total number. Is there an easy way to obtain the average and other metrics for each one? Some of this information I could probably find in my clunky (borderline boomer) way, by filtering, adding, and averaging values from the pairwise data (perhaps made easier by Predictome). Lastly, drawing rectangles on the PAE plot does a great job of giving coordinates and the average PAE, but it doesn’t give the range or other potentially useful data, such as the number of PAE<5 values etc. I guess I’m thinking that it could be very useful to be able to get metrics for a prescribed region of the PAE plot simply by drawing the rectangle. (And maybe there is but I missed it.) Those are my questions and thoughts. But I also wanted to express my gratitude for the ChimeraX software, and even more, the people working at ChimeraX who are always exceptionally responsive and helpful. David https://www.biorxiv.org/content/10.1101/2024.02.19.580970v1 https://www.biorxiv.org/content/10.1101/2024.10.23.619601v1 https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1 David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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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 30 Dec '24

30 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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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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Chimerax install error
by 王康瑞 11 Dec '24

11 Dec '24

Greetings! I'm a student from Tsinghua university, thank you for your contribution. I encountered a error when I installing ChimeraX, and I pasted it in the attach files below. I was able to launch chimerax with option"--nogui", and "--help" option seems run successfully too, but the ui didnt work. Thank you! Best wishes, Kyrie.

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Question about translating/rotating individual chains in a model
by John Watters 11 Dec '24

11 Dec '24

Hi all, I was wondering if anyone had any suggestions on how to rotate and translate a DNA-bound protein model one base pair at a time (essentially walking the protein down the double helix) so I can compare its interactions with another protein. My plan was to define a vector between the center of mass of each nucleotide pair to then move the DNA-bound protein one average pitch length using the move command and rotation using the turn command one nucleotide at a time. When I try to save these new models using "save pdf_filepath.pdb models #3 relModel #1" the DNA-bound protein is still in the original position - do I need to modify the save command or move the DNA-bound protein using different commands? Thanks for any help you can provide! Best, John

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chimeraX 1.9rc202412100000 and copy/paste from the log panel not possible
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, after upgrading to 1.9rc202412100000, I can't copy/paste a command from the log panel, typically the "view matrix" for the orientation. I tried it on 1.7 and it works with the 2 chimeraX sessions working at the same time. (haven't tried it on 1.8). Is there something specific I'm missing? I'm using macOS 14.6.1 Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Z-flip option for fitmap?
by Oliver Clarke 11 Dec '24

11 Dec '24

Hi, I frequently use fitmap with global search to quickly fit an initial model to low resolution EM maps at early stages of data processing. At low resolution, it is often not immediately obvious which hand of the map is correct, so I will fit to both the original map and one that has been Z-flipped. Would it be possible to add an option to do this automatically, similar to how the "resolution" flag fits a molmap of the model at the specified resolution to the map? Cheers Oli

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display pseudobonds between atoms as solid line
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model. I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands. I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0 but the distance does not appear on my screen. Could you help me work this out? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Connecting ChimeraX to Cytoscape via your structureVizX.zip file
by Jean-François Bureau 11 Dec '24

11 Dec '24

Hi, I already use Chimera to cytoscape and I would like to add chimeraX. I downloaded your structureViZ.zip file and open it but I did not find what to do next. Thank you for your help Regards JF Bureau Institut Pasteur Paris, France

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Mac with nogui to run batch cmd
by aponysbc＠gmail.com 10 Dec '24

10 Dec '24

Hi, I'm trying to generate images in batch with chimerax from terminal on mac m2. When I run "chimerax --nogui --exit --cmd" I get the error: raise LimitationError("Unable to save images because OpenGL rendering is not available") chimerax.core.errors.LimitationError: Unable to save images because OpenGL rendering is not available ChimeraX command "graphics driver" gives: OpenGL version: 4.1 Metal -88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Is there any way around this? I saw another post about this from 2020 that the nogui option only works on linux with offscreen. Is there any way to save images in batch from terminal? Thanks, Aaron

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Intra-chain contacts
by Rosaleen Calvert 10 Dec '24

10 Dec '24

Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy

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