- ChimeraX-users - RBVI Mailing Lists

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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Error during flipping to change the handedness of the cryo-EM map
by Shardul Dhole 10 Dec '24

10 Dec '24

Hi, I was trying to change the map's handedness while trying to fit two maps in ChimeraX. However, when I use the command vop flip #3 (3 is my model number), it gives an error: *"**Expected a density maps specifier or a keyword." * How to overcome this? Thank You. -- Regards, Shardul Dhole.

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ChimeraX 1.8 release
by Elaine Meng 10 Dec '24

10 Dec '24

UCSF ChimeraX version 1.8 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 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints 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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ChimeraX with Modeller
by Matt Goff 09 Dec '24

09 Dec '24

Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error: dyld[77819]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file) Exception in thread Thread-10 (threaded_run): Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff

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Installing ChimeraX in a Apptainer container
by tluchko 08 Dec '24

08 Dec '24

Hello, I am trying to install ChimeraX in an apptainer (singularity) container. I am able to load molecules but running into two issues. - I get a lot of python tracebacks (see below). I have also installed ChimeraX directly on the same machine from the RPM and do not see these error messages. - Rendering is very slow, so I don't think it is using the graphics card. The direct installation is similarly slow, but I have installed VMD on the same system and I can tell that it is using the graphics card, both from the log and the speed. Please let me know if you have any suggestions to address either of these issues. This is the command that I am using to launch ChimeraX apptainer exec --bind /tmp/.X11-unix,/storage/storage1 --env DISPLAY=$DISPLAY --nv chimerax-rocky9.sif chimerax This is the definition file for the container. BootStrap: docker From: rockylinux/rockylinux:9.4 %labels Maintainer Tyler Luchko Version 1.0 %help This is a Rocky Linux 9 container for ChimeraX 1.8 %setup # These are only required if running on the HPC. #mkdir -p ${APPTAINER_ROOTFS}/tmp mkdir -p ${APPTAINER_ROOTFS}/scratch %post echo "Installing packages into the Rocky Linux 9 container" dnf -y install yum-utils dnf -y config-manager --set-enabled crb dnf -y install epel-release dnf -y install mesa-dri-drivers glx-utils dnf -y install /tmp/ucsf-chimerax-1.8-1.el9.x86_64.rpm dnf clean all %environment export PATH=/usr/bin:/usr/sbin:/bin:/sbin export SHELL=/bin/bash export LANG=en_US.UTF-8 Sample error output is below. Thank you, Tyler NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1286, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/__init__.py", line 50, in start_tool return cmd.get_singleton(session, create=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/cmd.py", line 30, in get_singleton return tools.get_singleton(session, Log, 'Log', create=create) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 216, in get_singleton tinst = tool_class(session, tool_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 161, in __init__ from chimerax.ui.widgets import ChimeraXHtmlView ImportError: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 418, in start_tools bi.start_tool(session, tool_name) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) BUG: Tool "Log" failed to start: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( _See log for complete Python traceback._ NOTE: UCSF ChimeraX version: 1.8 (2024-06-10) NOTE: © 2016-2024 Regents of the University of California. All rights reserved. NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html) NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 138, in _delayed_register_log_recorder _register_log_recorder(session) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 172, in _register_log_recorder log.record_to_file(log_file) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ AttributeError: 'Log' object has no attribute 'page_source' BUG: Error processing trigger "new frame": AttributeError: 'Log' object has no attribute 'page_source' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ Sent with [Proton Mail](https://proton.me/mail/home) secure email.

3 3

Changing range for electrostatic potential coloring
by Eric Martz 07 Dec '24

07 Dec '24

I want to have less white and more color on an electrostatic potential map. I suspect this is done by reducing the range, but I can't find how to do this. I start with open 1bl8 fromDatabase pdb format mmcif select protein coulombic sel ui tool show "Surface Color" Then I have this dialog, where I have changed -10 ... +10 to -5 ... +5 When I click the Color button, I get "No map chosen for coloring", but the "using map" menu has no options. ??? Also I would like to re-color the surfaces for all 4 chains, not one at a time, but the "Color surface" menu seems to have 4 separate chain surfaces, but no option for all 4 at once. I will appreciate guidance! Thanks, -Erichttp://martz.molviz.org

3 5

Coloring charged amino acids
by Eric Martz 06 Dec '24

06 Dec '24

Consider this: open 1pgb fromDatabase pdb format mmcifstyle sphereshow atoms 1. What is the command to hide all water? 2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)? I was hoping there was a menu item or command that would do something similar to this: color all whitecolor :lys,arg bluecolor :glu,asp redcolor :his lightblue without having to type all those commands. FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar. Thanks, -Eric

2 2

Deleting hydrogen
by Eric Martz 05 Dec '24

05 Dec '24

I have studied the help delete.html but have been unable to guess the command syntax to delete all hydrogen atoms. Unfortunately, that help page has no examples. Please tell me the command. Thanks, -Eric

2 2

Centering?
by Eric Martz 05 Dec '24

05 Dec '24

I have spent over an hour failing to come up with the command that will move the molecule (and its center of rotation) to the center of the viewport. I see that "cofr all" places the center of rotation in the center of mass of what is loaded. But I have been unable to find the command to move it to the center of the viewport. I realize that I can drag it to approximate center of viewport with right-drag, but I'd like a command to do this. For example, load anything, drag it off center, then what is the command to move it back? Thanks, -Eric

2 1

duplicate the map view
by Vitali James 04 Dec '24

04 Dec '24

Dear Chimera users I have to make a slice of a map on the selected atom. Is it possible to duplicate this map view? in chimeraX James

3 5

Adding/editing chains' description
by André Graça 04 Dec '24

04 Dec '24

Hi everyone! I am missing a way to add/edit chain descriptions in ChimeraX. Is it possible? If not, would this be a reasonable request to plan for a future release? Wishing a nice day to whoever reads this message =) André ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Monday, December 2, 2024 10:52 PM To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 96, Issue 1 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 2 Dec 2024 13:52:23 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. To: Evan Kantrowitz <kantrow(a)bc.edu> Cc: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu>, chimerax-users <chimerax-users(a)cgl.ucsf.edu> Message-ID: <0368B293-FF58-4F72-97C0-51DF75D23035(a)cgl.ucsf.edu> Content-Type: multipart/mixed; boundary="Apple-Mail=_5630A7C6-3B74-4E39-A0F1-3F2D7DF8DDB0" Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html>> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets>> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>> More info, general explanation of model series vs. trajectories <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>> I hope this helps, 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 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-1.png Type: image/png Size: 44782 bytes Desc: not available -------------- next part -------------- > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu).-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-2.png Type: image/png Size: 113501 bytes Desc: not available -------------- next part -------------- > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz ----------------------------------------------------------------------------- ------------------------------ Subject: Digest Footer _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.…<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> ------------------------------ End of ChimeraX-users Digest, Vol 96, Issue 1 *********************************************

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ChimeraX Download
by Wagner, Elina Lynge 04 Dec '24

04 Dec '24

Hello, I have been trying to download ChimeraX but get the error message that x64 is needed. I currently have a Microsoft Surface Laptop 7th Edition. The processor is Snapdragon(R) X 10-core and the system type is 64-bit operating system, ARM-based processor. Even though I have the 64-bit operating system, will I be unable to download the program due to having an ARM processor? If this is correct, will there be a version of ChimeraX that will be able to run on new windows 11 computers (surface pro 11 and surface laptop 7)? Have a great day, Elina Lynge Wagner The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

2 1

Adding a label to MRC map file header
by Tom Goddard 03 Dec '24

03 Dec '24

Hi Raman, I'm not sure where in the MRC binary file this "EXPDATA EM" is suppose to go, maybe a "label" field. As you can see from the MRC file spec it has space for 10 labels in bytes 225-1024 of the header https://www.ccpem.ac.uk/mrc_format/mrc2014.php ChimeraX has no options to insert specified text into those labels, but you could edit the ChimeraX Python code that writes the MRC file to add a label. The file is called writemrc.py and is in your ChimeraX distribution, on Mac it is here ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/map_data/mrc/writemrc.py Here's what this code looks like in the ChimeraX Github repository https://github.com/RBVI/ChimeraX/blob/00c7ef34fdf8e3f9675cf892f346adbecbfe6… It has some lines that put a ChimeraX version and time stamp into the MRC file ver_stamp = 'ChimeraX %s %s' % (version, asctime()) labels = [ver_stamp[:80]] You could add a line after that labels.append('EXPDATA EM') to add a label with that string. then restart ChimeraX and save a map (e.g. command "save mymap.mrc"). Another approach would be to open the mrc file in a binary editor and carefully modify some of the bytes from 225-1024 to add your label. Of course all this assumes that EXPDATA EM is supposed to go in a label and not for instance the EXTRA bytes part of the header. It seems absurd that you have software that won't work without a special label in the file. Tom > On Dec 3, 2024, at 4:47 PM, Raman, C.S. <craman(a)rx.umaryland.edu> wrote: > > Hi Tom, > > Is there an easy way to insert into the header of an MRC file the descriptor "EXPDATA EM" as done by the PDB? I need to do this to run a validation program but don't quite know how to go about it. > > Any help would be greatly appreciated. > -raman

1 0

Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change.
by Elaine Meng 02 Dec '24

02 Dec '24

Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> More info, general explanation of model series vs. trajectories <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> I hope this helps, 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 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu) > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz -----------------------------------------------------------------------------

1 0

ChimeraX-1.8 functionality regarding the match command
by Nicholas Ferraro 02 Dec '24

02 Dec '24

Good morning, My name is Nicholas Ferraro. I am a graduate student at the City College of New York. I am currently using ChimeraX-1.8 to visualize multiple PDBs of the hexameric helicase I am working with. We have labeled each protomer of the hexamer A-F. I understand the software allows for matching structures either by best-aligning pair of chains, a specific reference structure to the best-aligning chain, and specific chains in a reference structure with specific chains in the matching chain. I have six PDBs. What I want to do is align all chains with respect to their chain ID and specific sequence. Can you advise on how to accomplish this in chimera-1.8? Thank you for you assistance. Please let me know if you need more details. Best, Nicholas Ferraro

2 1

Stepping through model in secondary structure element steps (ISOLDE)
by Vorländer,Matthias Kopano 28 Nov '24

28 Nov '24

Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender(a)imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP - Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org>

3 3

Re: IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by Tom Goddard 27 Nov '24

27 Nov '24

Glad you got it to work. Tom > On Nov 27, 2024, at 3:30 PM, LENKA MILOJEVIC <lenka11(a)g.ucla.edu> wrote: > > Dear Dr. Goddard, > > Thank you so much! That worked! I thought I’d have to produce a .cmm file or mask the map using the volume tool and the .mod file as a surface. > > I really appreciate your swift responses! This was incredibly helpful. > > Have a great rest of your day! > > Sincerely, > Lenka > > On Wed, 27 Nov 2024 at 15:26, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Lenka, >> >> Seems like you got what you wanted "I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD." Your image shows the traced curves as connected markers (fake atoms connected by bonds). To color the nearby density you would then use the Color Zone tool, menu Tools / Volume Data / Color Zone and it has a Split Map button that would let you make a new map that includes just the colored part near your curves. The equivalent ChimeraX command is "color zone" >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone >> >> If the command syntax is confusing just use the graphical Color Zone tool and it will log the equivalent command to the Log panel and you will have a better idea of how to type a command if you want to use some of the fancier options (like bondPointSpacing) that the graphical tool does not offer. >> >> Tom >> >> >>> On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> In the event that I want to mask map #3 using the .mod file in #1 , which command exactly do I run? I'm attaching a screenshot showing my current session. >>> <image.png> >>> >>> >>> On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <lenka11(a)g.ucla.edu <mailto:lenka11@g.ucla.edu>> wrote: >>>> Hi Elaine, >>>> >>>> If I don't input contours true, nothing shows up on my screen. It just states it read it. >>>> open <> C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod >>>> Read IMOD model C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod, pixel size 0.568 >>>> >>>> Sorry for the trouble. I really appreciate your help. >>>> >>>> Best, >>>> Lenka >>>> >>>> On Wed, Nov 27, 2024 at 2:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> Hi Lenka, >>>>> Contours true is to make it into markers and links (fake atoms and bonds) instead of a surface. You do not need markers and links for masking, you only need a surface model (meshes true contours false). >>>>> >>>>> Just open the file directly without any options and by default it should make a surface model that you can use in "volume mask" - I thought "meshes true" would still make the surface but maybe it only does that when contours is false. >>>>> >>>>> I'm sorry I mentioned the contours option since it was confusing... I only did so because at first I thought you wanted markers. >>>>> >>>>> I hope this helps, >>>>> 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 Nov 27, 2024, at 1:34 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Dear Dr. Meng, >>>>> > >>>>> > Thank you! I've now managed to open the segmentation with open C:Path format imod meshes true contours true. But If I run volume mask it just outputs: >>>>> > volume mask #3 surfaces #1 fullMap true >>>>> > No surfaces specified >>>>> > volume mask #3 #1 extend 3 >>>>> > Missing required "surfaces" argument >>>>> > volume mask #3 surfaces #1 >>>>> > No surfaces specified >>>>> > >>>>> > Any advice? Is the contour not actually a surface yet? Or am I writing the command wrong. >>>>> > >>>>> > Thank you so so much! >>>>> > >>>>> > Best, >>>>> > Lenka >>>>> > >>>>> > On Wed, Nov 27, 2024 at 1:45 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> > Hi Lenka, >>>>> > The link that you sent is to the Chimera documentation (not ChimeraX): >>>>> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> >>>>> > >>>>> > Since they are different programs, there are differences... but not in this case! ChimeraX can also open these IMOD segmentations: >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> >>>>> > >>>>> > These segmentation models are surfaces, not the atoms or pseudoatoms (markers) that you would need to define a zone with Color Zone. Although the second link above explains that you can make the IMOD surface mesh into markers/links by opening the file with the "open" command option "contours false," that is unlikely to make them suitable for defining zones. Mainly it is used to improve display. >>>>> > >>>>> > Instead you can use "volume mask" to mask parts of your map with the IMOD segmentation surfaces. >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> >>>>> > >>>>> > I hope this helps, >>>>> > 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 Nov 27, 2024, at 11:56 AM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > > >>>>> > > Dear Sir or Madam, >>>>> > > >>>>> > > While the 'Input File Types' page lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. >>>>> > > >>>>> > > I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. >>>>> > > >>>>> > > I appreciate your time and assistance! >>>>> > > >>>>> > > Sincerely, >>>>> > > Lenka >>>>> > >>>>> > _______________________________________________ >>>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>

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IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by LENKA MILOJEVIC 27 Nov '24

27 Nov '24

Dear Sir or Madam, While the 'Input File Types' page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. I appreciate your time and assistance! Sincerely, Lenka Lenka Milojević Biophysics PhD Candidate Z. Hong Zhou Lab University of California, Los Angeles

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Closest distance list between residues/atoms; And selecting first/last residue in a chain
by pm676＠cam.ac.uk 27 Nov '24

27 Nov '24

Hi Is there a way by command line to generate a list of residue to residue (or atom to atom) distances ranked by closest to furthest, for say, all residues within 4A of each other at an interface between two protein chains? Can it also state the type of interaction, e.g. salt bridge, H-bond, vdW? Also, completely separately, is there a way by command line to select the first and last residue in a chain (without having to find their number)? No worries if not. Thanks so much! Cheers, Paul

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Visualization of methyls rotations
by Enrico Martinez 27 Nov '24

27 Nov '24

Dear ChimeraX users! In visualizing the MD trajectory, I noticed a small issue with the depiction of the rapid rotations of the ligand's methyl groups. Specifically, the hydrogens appear to periodically collapse into a singularity before returning to their expected positions. Could this be addressed through additional post-processing of the trajectory data? Many thanks in advance Enrico

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Question about using AF3-competitor outputs
by David S. Fay 26 Nov '24

26 Nov '24

Hi, Apologies if this already came up and I missed it. I just ran a few dimer models on the Chai Discovery website (https://lab.chaidiscovery.com/dashboard) and it seems to work quite well. However, when I tried to upload the relevant json file using the Structure Prediction - AlphaFold Error Plot pulldown menu, ChimeraX failed to recognize the file. I tried a few other files and something similar happened. Do you know of a workaround or is this something that is likely to get patched soon? I should mention that Chai may be putting the relevant PAE information into a “npy" file, (e.g., pae.model_idx_0.rank_1.npy) based on the size of that file, and I haven’t yet tried to convert npy to a json or know if that’s even possible. I also wonder if Boltz-1, another AF3 competitor, will have different outputs as well. They don’t seem to have a GUI yet and perhaps they won’t, so I haven’t been able tyo test this yet. I assume this has all been topic of discussions at ChimeraX though… Thanks in advance for your help! David 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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How to remove specific H bonds
by Sen, Anindito 26 Nov '24

26 Nov '24

Dear ChimeraX group, How do I remove certain 'H' bonds from an atomic model, leaving the important 'H' bonds Regards Stay safe & Regards Anindito Sen. Ph.D

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Some questions about electrostatic potiential surface
by Quek 26 Nov '24

26 Nov '24

Dear Administrator, May I ask why the electrostatic potential surface I generated in Chimera X is entirely red without any blue? Is it because the electrostatic range is not set correctly? Could you tell me in which module I can set the range for the electrostatic potential? Additionally, how can I display the color scale for the electrostatic potential? Looking forward to your reply. Quek 1171543499(a)qq.com  

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RMSD between nonidentical atomic models
by Roden Deng Luo 26 Nov '24

26 Nov '24

Hi, If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case. I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models. 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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ChimeraX opening failure
by gianmarco.elisi＠gmail.com 25 Nov '24

25 Nov '24

Dear users, ChimeraX fails to open with multiple installation versions. The error with debug option that is shown is the following: Starting main interface Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-SelInspector True None Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=e42ced0f-7162-57b1-9d35-4f49e… Toolshed: find_bundle ChimeraX-Core True None Windows fatal exception: access violation Thread 0x00004b9c (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\socket.py", line 836 in create_connection File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 945 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1451 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 979 in send File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1041 in _send_output File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1281 in endheaders File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1332 in _send_request File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1286 in request File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1348 in do_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1391 in https_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 496 in _call_chain File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 536 in _open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 519 in open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 216 in urlopen File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 467 in reload_available File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 975 in run File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 995 in _bootstrap Current thread 0x00005d04 (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 315 in event_loop File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1003 in init File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Any suggestion? Thanks

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Overlay of specific chains
by Reza Khayat 25 Nov '24

25 Nov '24

Hi, We have multiple structures of a homo-hexamer (chains A-F). We'd like to overlay limited regions of each chain onto equivalent chains (e.g. residues 200-452 of chain A onto residues 200-452 of chain A). We're having difficulty identifying the correct syntax. Some of our structures align as desired while others are aligned according to the chain combinations that produce the lowest RMSD (e.g. residues 200-452 of chain A align onto residues 200-452 of chain C. Is it possible to restrict which chains align to which? Best wishes, Reza

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VR on Apple silicon?
by David Bhella 22 Nov '24

22 Nov '24

Has anyone managed to make chimeraX VR work on an ARM Mac with meta quest 3? Possible or am I flogging a dead horse? D Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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protein void volume or enclosed space
by Vitali James 21 Nov '24

21 Nov '24

Dear Chimera support, Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x. best, James

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