- ChimeraX-users - RBVI Mailing Lists

Surface Color
by Hansen, Bryan (NIH/NIAID) [E] 24 Jan '25

24 Jan '25

Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Assigning a custom net charge for a ligand using dockprep
by Jade Shi 24 Jan '25

24 Jan '25

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly? Thanks a lot! Jade

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Draw and build secondary structures interactively
by Roden Deng Luo 22 Jan '25

22 Jan '25

Hi, I know there is a tool and command "build". But it is not that interactive. I wonder if there is a feature in ChimeraX (or any other tools) that can allow the user to draw in 3D space (or 2D) lines and then specify some segments as alpha-helices and some other segments as beta-sheets. I imagine the generated structure can be a backbone populated with G (glycine). 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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"forEach" command to open multiple pdb from multiple directories and save images there ?
by Vincent CHAPTAL 21 Jan '25

21 Jan '25

Hi, I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. I'm using the forEach command to open all the results and run the script to create an image, and it works very well: open script.cxc forEach /PATH*/ranked_*.pdb script.cxc: open reference-structure.pdb match #1 to #2 color #*/B green color #*/C red color #*/D blue view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41 I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location: save /PATH*/$file.png doesn't work because the /PATH*/ is not recognized as an existing directory. save /$PATH*/$file.png gives the same error. If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. Could you let me know how to save in the folder where the .pdb was read from? 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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UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

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Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

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No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

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Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

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Question about the tool Find Cavities
by svle＠tiscali.it 16 Jan '25

16 Jan '25

Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio

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pb with alphafold error plot when we used dimer
by Jean-François Bureau 15 Jan '25

15 Jan '25

Hi, When I stimulate dimer using alphafold3, it is not possible to load the error plot since Chimerax is waiting to have the data of the first protein and find that of both. Best JF Bureau

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Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
by Elaine Meng 13 Jan '25

13 Jan '25

Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, 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 Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2(a)gmail.com> wrote: > > Oh shoot! > You are right, > > I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html > I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced. > > Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow. > > This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf > > THANK YOU for answering on a Sunday!! > Anne-Frances > >

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abbreviation for transparentbackground please
by Anne-Frances Miller 12 Jan '25

12 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Problem upgrading to the latest version 1.9
by svle＠tiscali.it 09 Jan '25

09 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

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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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