- ChimeraX-users - RBVI Mailing Lists

Subtracting Two Surfaces (.cube files) for Calculating Fukui Functions
by fsl＠displ.nl 15 Jan '26

15 Jan '26

Hello all, I'm trying to calculate Fukui functions [1] using orca, I'm trying to recreate the plots mentioned in [1] as well. Briefly, I have generated two surface files f_n+1.cube and f_n.cube. I tried running in ChimeraX's console ``` open f_n+1.eldens.cube format cube open f_n.eldens.cube format cube volume subtract #1 #2 ``` But I get is a histogram on side with the level slider, and none of the levels match with the output figure on [1]. I'm not sure how to proceed ahead. Am I missing something, isn't there a surface subtract? rather than volume subtract. The files I used for the plots are in [2]. Regards hisacro. [1]: https://www.faccts.de/docs/orca/5.0/tutorials/react/FUKUI.html [2]: https://displ.nl/pb/lactone2.tar.xz

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Zones help
by Timothy Springer 14 Jan '26

14 Jan '26

I am analyzing a complex made with Alphafold with 7 protein subunits and am trying to find all the interchain contacts. The zone command is useful select zone #1/A 3.6 #1 residues true, but how can I make it find all interchain contacts at once, rather than one chain at a time? What is a command to display sidechains of all residues in the zone? I really like the PAE plot that ChimeraX makes from alphafold predictions. Could I make a similar plot of the contact residues made with the zone command? - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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ChimeraX New User Inquiry on Superimposing Proteins
by Hsueh, Vincent 12 Jan '26

12 Jan '26

Good morning UCSF ChimeraX Support Team, My name is Vincent Hsueh and I'm a P1 Pharmacy Student at Champan University. I'm a new member to the lab and it seems no one, currently with the lab, has prior experience to using ChimeraX. So far, I have isolated the Human ACE hAChE (PDB: 3LII) in the .csx file attached to the email. My PI gave me the task to superimpose to proteins, Human AChE (PDB: 3LII) colored in Beige and hTg ChEL (PDB 6SCJ) colored in Gold, but I'm having issues learning how to do it on my own. I'm trying to isolate Chain #B from PDB: 3LII with PDB: 6SCJ to see which part of 6SCJ is adjacent to 3LII prior to isolating both chains. I tried reading the ChimeraX user guide, and created the attached "in-progress(super-imposed)_final.csx file, but I'm still not sure how to do it properly. So far, I've opened my isolated PDB: 3LII model in ChimeraX, opened the PDB: 6SCJ file, used the matchmaker command, highlighted the corresponding sequences in SequenceViewer, but my PI has told me that the resulting model still has minor issues. Hopefully, I can gain some guidance in this effort to learn ChimeraX on my own, for my lab, and for future lab members! Vincent Hsueh PharmD Candidate Class of 2028 Chapman University School of Pharmacy vhsueh(a)chapman.edu<mailto:catvu@chapman.edu>

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Determine angle and axis while using Matchmaker
by Sen, Anindito 08 Jan '26

08 Jan '26

Dear All, I have 2 models of a protein positioned in different places in a complex macromolecular assembly. Using Matchmaker I can align the 2 models. How can I get the angles and the axis of rotation/orientation that is calculated to align the 2 models in Matchmaker. Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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how to make a contour plot from Gaussian16 cube file
by Steven Brawer 07 Jan '26

07 Jan '26

I have used Chimerax for proteins, and it is indeed wonderful. However, now I would like to use it to view output from the Gaussian16 "computational chemistry" program, and I am at a loss. I believe the "volume" command is what I need, but I have a LOT of trouble understanding the terminology of the user documentation for the "volume" command. Perhaps someone can be very specific and guide me in the particular procedure described below (or tell me Chimerax does not do such a thing). I have a Gaussian16 cube file for electron density. (This is electron density on grid points. Chimerax can read this file.) I would like to make a contour plot - say contours in the xy plane at z = 0. I would like to specify the number of contours. I would like to know the distance (in au units) of any point on a particular contour from the origin (x=y=z=0) or even from some arbitrary point in space. I would like some sort of legend indicating the density value of each contour. How can I set this up? It would also be nice to be able to specify any plane. Thanks very much Steve

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Measuring contact area in a pdb file
by Shimberg, Geoffrey (NIH/VRC) [C] 07 Jan '26

07 Jan '26

Dear ChimeraX Developers, I was wondering if you could explain to me how to measure the contact residues/area in a pdb file containing an antibody and antigen? I have been trying to do either measure buriedArea or contactArea, but I get an error. I have been using the PDB file 7Y0W as a starter structure to then use for future structures. Let me know if you need anything else. Thank you for all your help. Geoffrey Shimberg

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Surface overlapping with atomic model
by naeshi9min＠postech.ac.kr 07 Jan '26

07 Jan '26

Hi, I'm Gumin Han from South Korea. Thank you for your wonderful visualization tools. This is my first time writing a question here. I want to overlap my models with surface as shown in the link (Figure panel B) https://www.nature.com/articles/s41467-024-49516-2/figures/1 Which options should I use? Thank you for reading my E-mail and best wishes for the New Year' Best regards, 2026, Jan 7th Gumin Han

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Trouble installing ISOLDE in ChimeraX
by Heng Jiang 06 Jan '26

06 Jan '26

Dear ChimeraX Support Team, I hope this message finds you well. I am currently trying to install the ISOLDE plugin in UCSF ChimeraX via Tools → More Tools…, but unfortunately, the installation does not work. I have attempted multiple approaches, but the “More Tools” window does not open. Could you please advise if there is an alternative way to install ISOLDE, such as an offline installation method or by providing the necessary plugin files directly? Thank you very much for your time and assistance. I look forward to your reply. Best regards, Heng Jiang

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Is toolshed down?
by jurkeviciute.gabija＠gmail.com 06 Jan '26

06 Jan '26

Hi, Apologies to bother, but I cannot seem to access toolshed to install isolde on either chimerax 1.11 or my web browser. I checked in with some colleagues and they reported the same thing. Is the site down for the toolshed by any chance? Thanks! Gabija

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Video Tutorial on Protein Interaction Modeling
by David S. Fay 05 Jan '26

05 Jan '26

Hi Everyone, Despite not really being qualified, I’ve done several protein modeling workshops at universities over the past year with some positive responses. It seems to be quite useful to a good number of scientists like myself (clueless molecular/cellular biologists etc), and in particular for less experienced users. Part of my ability to pull this off at any level has been the help I’ve received from others including the wonderful staff the ChimeraX, who I give ample props to in the video. Anyway, feel free to share with students or others who might find this useful. It’s rather long (97 minutes) and I do go into a fair bit of detail about how ipTM is determined along with some of the recently developed alternative metrics for scoring protein-protein interactions. I’ve attached the link below. I also realize that this user group is very sophisticated, so feel free to comment or correct and to add to anything I may have missed or not stated properly. Thanks and happy new year, David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu<mailto:davidfay@uwyo.edu> <https://youtu.be/u63oYfWDBoM> [maxresdefault.jpg] David's AlphaFold WorkShop 2026<https://youtu.be/u63oYfWDBoM> youtu.be<https://youtu.be/u63oYfWDBoM>

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