- ChimeraX-users - RBVI Mailing Lists

"H-Bonds" Tool Displays Non-H Bond Bonds?
by Melisa Kalaba 15 May '24

15 May '24

Hello. I wanted to display the hydrogen bonds between my ligand and protein, however when I hovered over the displayed bonds with my cursor I noticed one of the bonds being between two nitrogen atoms and I was confused. Is this a bug within the software? I'll attach a screenhot so you can take a look at it yourself: https://drive.google.com/file/d/1N5YRncOrrJnEVRpM8XD7O1tPG02ZTu8G/view?usp=…

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Missing-structure labels
by Eric Pettersen 15 May '24

15 May '24

Hi all, In the 1.9 daily build only (not the 1.8 release candidate), missing-structure pseudobonds are now labeled with the number of residues the pseudobond represents. If you do not like this new behavior, you can turn it off in the 'Labels' preference category (make sure to 'Save' your changed setting). --Eric Eric Pettersen UCSF Computer Graphics Lab

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Alphafold3 models
by Allen Place 15 May '24

15 May '24

I just ran Alphafold3 predictions on our dinoflagellate pks proteins. Will chimerax read the models which are .cif files? I want to highlight the various domains in the 3D models. I am running on OSx. Al Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place(a)umces.edu ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful” He is smart, makes friends easily, and never loses his sense of humour. He thrives on a challenge Sign up to receive our quarterly newsletter, Inside IMET!

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Cofr command output in log
by Kumpula, Esa-Pekka 14 May '24

14 May '24

Dear ChimeraX crew, A minor quality-of-life improvement request: would it be possible to have the command cofr output the values as a comma-separated list instead of a whitespace separated one? I am including cofr information reatively often in my figure preparation scripts and having NOT to always replace these when copy&pasting would be a nice improvement! Also, in general, can I customize the output of commands to the log (such as view matrix, cofr, zoom, clip list) within an alias for example? In a fluffy dream world, I would have an output from these that I can directly copy&paste to my scripts and get the camera positioned Just Right. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Feature request for .glb files
by Leonardo BETANCURT ANZOLA 14 May '24

14 May '24

Hello! I am currently exporting .glb files so I can add them to a Keynote presentation and would like to keep the labels for the amino acids. When I see the file, the letters are in 2d, do you know if there is a way to add a little bit of depth to the letters when exporting such a file? I added a video that shows how the labels are invisible from some points of view Also, it would be awesome if files could be exported in .usdz so they can be easily added to Keynote Thank you, Leo B

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Fwd: Inquiries on UCFS Chimerax
by Tom Goddard 14 May '24

14 May '24

Please send ChimeraX questions to the mailing list unless they contain private data. Begin forwarded message: From: ahmed morsy Subject: Inquiries on UCFS Chimerax Date: May 7, 2024 at 4:52:22 AM PDT To: "goddard(a)cgl.ucsf.edu" Reply-To: ahmed morsy Dear Dr. Thomas Goddard, I hope this message finds you well. I am very thankful for your great tutorial on the UCFS Chimerax YouTube channel. I have a few questions that need your kind response: 1- Can we apply UCFS Chimerax for detecting the interaction between protein & ligand, or small molecule (from Pubchem library) and protein? 2- What is your standard for increasing or decreasing C-alpha distance (in Angestrom) to color the structure that is different between the Alphafold prediction and the experimental one? Thank you for reading my message, and I look forward to hearing from you. Best regards, Ahmed Morsy ========================= Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea Tel.: 02-450-0498 C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Re: Protein-ligand interactions
by Guillaume Gaullier 14 May '24

14 May '24

Hello Ahmed, I am not aware of any formal standard for figures, at least in my field, beyond the specific technical requirements of different journals (certain preferred image formats with a certain minimal resolution in DPI, etc.). In practice, the reviewers will complain if they find the figures confusing. So the best you can do initially is to use your judgment as to whether the figures show what you want to communicate. It is often very enlightening to run the figures past colleagues who were not involved in the project and see what their first reaction is (do they immediately get what you are trying to show? do they get confused? can they suggest ways to clarify the figures?). Then once you get feedback from reviewers, what needs to be changed typically becomes clear. Regarding aesthetics, pretty much anything goes as long as it doesn’t confuse the message the figure is meant to communicate. In certain fields, there are conventional color codes that have been in use for a long time, and it often facilitates communication with this research community to follow their conventions (even though nobody can force you to do it; a reviewer could suggest it but I believe it would be wrong for them to make it a strict requirement). But this is never advertised anywhere, you need to find out by reading the literature of this specific field. It is always good if figures are reproducible, and I like using ChimeraX’s command scripts for that (see some examples from my own work here: https://github.com/Guillawme/chimerax-viz ). I hope this helps, Guillaume On 11 May 2024, at 16:17, ahmed morsy via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. Dear Dr. Meng, I hope this message finds you well. I am writing to you as we are planning to utilize ChimeraX for structural analysis in our upcoming research projects. As we prepare to integrate ChimeraX into our workflow, we are particularly keen to ensure that our approach and the resulting figures are in line with scientific standards and will be well-received by the academic community. To this end, we would greatly appreciate if you could provide us with any references or examples of published research where ChimeraX has been used for similar purposes. Specifically, we are looking for insights into how figures generated using ChimeraX have been formatted and validated in peer-reviewed publications. We aim to adhere closely to best practices and ensure that our use of ChimeraX enhances the credibility and scientific rigor of our findings. Any guidance, examples, or recommendations you could share would be immensely helpful. Thank you for your time and support. We look forward to your response and any assistance you can provide. Best regards, Ahmed Morsy On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Dear Ahmed Morsy, (1) Depends what you mean by "detecting" ... if you mean will it dock the ligand with the protein to predict where/how it binds, the answer is no. If you mean you already have a structure of a ligand-protein complex (such as from experimentally determined structures or the output of some other protein-ligand docking program), then the answer is yes, you can use ChimeraX to analyze the interactions. For examples of what you could do, see the "protein-ligand binding sites" tutorial: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> See also the ViewDockX tool for looking at results output from other programs that do protein-ligand docking: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> (2) there is no standard. You have to use your own scientific (and for a paper figure, artistic) judgment, based on what you are trying to show and the details of the proteins you are interested in. 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 May 7, 2024, at 10:45 AM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Please send ChimeraX questions to the mailing list unless they contain private data. > > Begin forwarded message: > > From: ahmed morsy > Subject: Inquiries on UCFS Chimerax > Date: May 7, 2024 at 4:52:22 AM PDT > To: "goddard(a)cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>" > Reply-To: ahmed morsy > > Dear Dr. Thomas Goddard, > > I hope this message finds you well. > I am very thankful for your great tutorial on the UCFS Chimerax YouTube channel. > > I have a few questions that need your kind response: > > 1- Can we apply UCFS Chimerax for detecting the interaction between protein & ligand, or small molecule (from Pubchem library) and protein? > 2- What is your standard for increasing or decreasing C-alpha distance (in Angestrom) to color the structure that is different between the Alphafold prediction and the experimental one? > > > Thank you for reading my message, and I look forward to hearing from you. > > Best regards, > Ahmed Morsy > ========================= > Ahmed Morsy, Ph.D. > > Assistant Professor, > Department of Stem Cell & Regenerative Biotechnology, > Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea > Tel.: 02-450-0498 > C.P.: +82/10-5299-5844 > E-mail: ahmed_morsy86(a)yahoo.com<mailto:ahmed_morsy86@yahoo.com>; ahmed(a)konkuk.ac.kr<mailto:ahmed@konkuk.ac.kr> > Orcid id: https://orcid.org/0000-0003-3873-9903 > Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) > Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem > GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en > _______________________________________________ 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/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Questions about ChimeraX
by Joshua Hori 13 May '24

13 May '24

Hello ChimeraX, I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats. I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms. Sincerely, Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly<https://calendly.com/d/ytt-hsj-vbn>

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Re: Alphafold 3
by Tom Goddard 13 May '24

13 May '24

Oliver Clarke points out that VP of research at DeepMind, Pushmeet Kohli, says they hope to release AlphaFold 3 code in 6 months. "We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months. Pushmeet Kohli. 11:27 AM · May 13, 2024" https://x.com/pushmeet/status/1790086453520691657 If that happens we will try to add ChimeraX support for running AlphaFold 3 predictions. Tom > On May 13, 2024, at 1:42 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi Tom, hope all is well! It seems like this stance might change (maybe because of all the pushback from the community?): > > https://x.com/pushmeet/status/1790086453520691657 > > So maybe it will be possible by the end of the year... > > Cheers > Oli > >> On May 13, 2024, at 4:23 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Sohail, >> >> Google did not released the code for AlphaFold 3 so the only way to run it is from their web page. They also have not provide a web service that would allow programs like ChimeraX to submit prediction jobs. I asked a contact at Google DeepMind if they plan in the future to provide a web service or provide the code, and they said they have no plans to do so at this time. Details here >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15135 >> >> Google also is not allowing researchers to run predictions with small molecule ligands except for some very common ones like ATP. It appears Google is treating AlphaFold 3 as a commercial product so the most useful capabilities will only be accessible to the drug discovery company Google has formed called Isomorphic Labs. >> >> I will be making the ChimeraX display of predicted aligned error (PAE) work with AlphaFold 3 output. Currently it is broken because AlphaFold 3 now has predicted aligned error for individual atoms of ligands, ions, glycosylation and non-standard residues while AlphaFold 2 only had values for residues of proteins. I expect to put this fix in ChimeraX today or tomorrow and it will be in the ChimeraX daily builds and ChimeraX 1.8 release candidates. >> >> Tom >> >> >> >> >>> On May 11, 2024, at 6:18 AM, Khawar Siddiqui via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi, >>> Greetings! When ChimeraX will get Alphafold 3? >>> >>> Thanks and best wishes >>> >>> Dr K Sohail Siddiqui, >>> School of Biotechnology and Biomolecular Sciences (BABS), >>> Room 420, Building D26, >>> The University of New South Wales (UNSW), >>> Randwick, High Street, Sydney, Australia. NSW 2052 >>> Office: +61 2 938 55193 <tel:+61 2 938 55193> >>> email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com >>> _______________________________________________ >>> 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://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> _______________________________________________ >> 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://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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Alphafold 3
by Khawar Siddiqui 13 May '24

13 May '24

Hi, Greetings! When ChimeraX will get Alphafold 3? Thanks and best wishes Dr K Sohail Siddiqui, School of Biotechnology and Biomolecular Sciences (BABS), Room 420, Building D26, The University of New South Wales (UNSW), Randwick, High Street, Sydney, Australia. NSW 2052 Office: +61 2 938 55193<tel:+61%202%20938%2055193> email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com

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Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How can I modify the palette of alphafold?
by Xiaohua Hu 09 May '24

09 May '24

I run command "color bfactor #1 palette alphafold", but I think the color is not so good. How can I modify or redefine the palette alphafold?

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ChimeraX / Alphafold docking question: Heterodimer and ligand
by Anthony Newcombe 08 May '24

08 May '24

Hello I'm currently evaluating ChimeraX for non-commercial use. I'm interested in predicting a complex of an unknown ligand to a heterodimer (receptor) with a known structure, pdb file available. The help files mention: *For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains)* If I download the structure of the heterodimer first, does this mean I can then select this then add the primary sequence of the ligand to try to dock? If not, can I add all the primary sequences and tick 'use PDB templates when predicting structures'? Would this then use the known experimental structure of the receptor? I hope this makes sense and thanks for the help Best wishes Tony Anthony Newcombe Ballinascarthy Clonakilty Cork Ireland

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Fwd: registration issue
by Elaine Meng 08 May '24

08 May '24

Hi Stephen, For questions that don't relate directly to commercial licensing, please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (already CC'd here so you don't need to do it) or chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> .... I don't know the answer to your question but the people on those lists would be your best bet. See the "contact us" page: <https://rbvi.ucsf.edu/chimerax/docs/contact.html <https://rbvi.ucsf.edu/chimerax/docs/contact.html>> If I had to guess, I would say that our server was temporarily down and that as soon as it is up (which may actually be the case), your registration attempt will "take" and you won't be prompted again in the near future. As the dialog says, please try again, although I know it's annoying if the server is still down. Maybe somebody on our team can respond as to whether it is up now? In the meanwhile, very sorry for the inconvenience and wasted time filling out the form. Best 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 > From: Stephen Miller <miller.stephen(a)gene.com <mailto:miller.stephen@gene.com>> > Sent: Monday, May 6, 2024 3:14 PM > Subject: registration issue > > Hello, I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello, > > I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration server is unavailable, and then the notification pops up the next time I launch the program. > > Is there something I can do to get this done properly? Thank you for any help! > -Steve > >

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Re: [Chimera-users] Chimera scripting
by Elaine Meng 07 May '24

07 May '24

Hi Flip, If you save a PDB file from ChimeraX it will save the current helix and strand assignments of the protein and peptide residues (as HELIX and SHEET records). I'm not sure if that is what you were saying is missing, or how you determined that they were missing. It does not save, however, helix type or which sheets the strands belong to. Elaine > On May 7, 2024, at 11:29 AM, Flip Jansen <f.bastiaanjansen(a)gmail.com> wrote: > > Hi Elaine, > > Thank you that is very clear! > > As for the second point, I meant preserving secondary structure information when saving an adapted PDB file in Chimera. I am now planning on using PyMOL for this purpose. > > Thanks again for your help! > > Best, > Flip > > On Mon, May 6, 2024 at 11:56 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Flip, > (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. > > (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> > > (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > Hello Chimera dev team, > > > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > > > Best, > > Flip Jansen >

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Guidance on aligning models with overlapping aa subsequences
by Martin Gordon 07 May '24

07 May '24

Hi everyone, I'm hoping to get some assistance from the community for visualizing structures from multiple AF runs with overlapping subsequences. We have been using AlphaFold monomer to try to identify structure and domains of a large (+3000aa) human protein. Our AF runs fail to model the full structure (possibly insufficient resources), so we have tried 'breaking' up the protein into overlapping subsequences. I was wondering if there is a sensible way to combine these substructures based on their overlapping regions? I have tried matchmaker, which I believe constructs a MSA and attempts to align the structures, but it seems a significant region of the overlap is not aligning correctly (img below with the overlapping subsequences highlighted). Any guidance is greatly appreciated. Thank you, Martin [image: image.png] Thank you, Martin

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Inquiry on the vertex_convexity function
by Yoseph Loyd 07 May '24

07 May '24

Hi ChimeraX Team, My name is Yoseph, I'm a student. I saw that your measure convexity function 'vertex_convexity' is documented to report the vertex convexity from ' 2pi - half cone angle of the incident vertex and all triangles the incident vertex is a part of'. Is the half cone angle generated by averaging all half cone angles? Thank you for taking the time to read this and I hope your day goes well. Best regards, Yoseph Loyd

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Making movie of whole cell model with EM images
by George Schaible 07 May '24

07 May '24

Hello, My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you! -- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>

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No version number in Add- Remove Program (Windows)
by Gruhm, Sebastian 07 May '24

07 May '24

Hello, I manage the software distribution at the Frei Universität Berlin, and I noticed that after installing ChimeraX 1.7.1, the entry in "Add-Remove Programs" (ARP) does not include a version number (see attached Screenshot). This is problematic because I cannot create a query for the version number in the software distribution (SCCM). All that would need to be done to display the version number under ARP is to create the RegKey "DisplayVersion" under "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\UCSF ChimeraX_is1". Would be great to see this implemented in the next version of ChimeraX. Mit freundlichem Gruß Sebastian Gruhm [cid:image001.jpg@01DAA061.0DA8A940] Zentraleinrichtung für Datenverarbeitung Server Infrastructure (SI) Fabeckstraße 32, 14195 Berlin Raum: 110 Phone: +49 30 838 58668 sebastian.gruhm(a)fu-berlin.de

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Adjust the Rotation Axis Size in ChimeraX
by AARON FERRELL 07 May '24

07 May '24

Hello, Is there a way to adjust the size of the rotation axis generated by the command line "measure rotation #2 toModel #1, in ChimeraX? I am looking to adjust both the length and diameter of the axis display. Please let me know! Best, Aaron

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Issue with Recurring Update Notifications in ChimeraX
by ahmed morsy 07 May '24

07 May '24

Dear ChimeraX Support Team, I hope this message finds you well. I am writing to ask for help with an ongoing issue I've been having with ChimeraX. Despite having downloaded and installed the most recent version of ChimeraX, I continually receive prompts to update the software each time I launch it. This occurs even though I am certain I am running the latest version. Could you please help me understand why this might be happening, and advise on how to resolve this issue? It would be helpful if you could provide steps or recommendations to ensure that the software recognizes the current version installed on my system. Thank you for your time and assistance. I look forward to your prompt response. Best regards,Ahmed Morsy=========================Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology,Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaTel.: 02-450-0498C.P.: +82/10-5299-5844E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Alphafold
by Chang, Jufang 06 May '24

06 May '24

Dear Sir Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? Thank you Ju-Fang ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Amber output pdb file - can't open... bad PDB record
by Alexander Hung Lee 06 May '24

06 May '24

Hi! I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore. Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 1

Re: [Chimera-users] Chimera scripting
by Elaine Meng 06 May '24

06 May '24

Hello Flip, (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera dev team, > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > Best, > Flip Jansen

1 0

session files question
by Krishnan Raman 06 May '24

06 May '24

I have two large session files (1-2 GB). Is there any way to combine them ? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 2

Error when opening multiple tiff stacks (32-bit)
by Christophe Leterrier 03 May '24

03 May '24

Hi, I have two 32-bit tiff stacks (generated by ImageJ) and I try to open both to overlay two channels. When opening the second one or trying to open both at the same time (see paths below), I get the following error with the latest stable and daily ChimeraX macOS versions: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch1_ph647_bas643_sypto_map_3D_48K_DC1C_(22688,12672)_TS3D.tif" "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch2_ph647_bas643_sypto_map_3D_7,63K_DC1C_transfo_(22688,12672)_TS3D.tif"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/open_command/dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 191, in provider_open models, status = collated_open(session, None, paths, data_format, _add_models, log_errors, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/__init__.py", line 182, in open return open_map(session, path, format=_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3621, in open_map smodels, smsg = open_grids(session, sgrids, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3723, in open_grids v.update_drawings() File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 813, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 633, in initial_image_levels mstats = self.matrix_value_statistics() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1734, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1769, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1252, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1276, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/griddata.py", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 74, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 199, in planes_data a = tif.asarray(key = plist) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 4272, in asarray pages = pages._getlist(key) ^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in _getlist pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in <listcomp> pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7578, in _getitem self._seek(key) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') IndexError: index out of range IndexError: index out of range File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') See log for complete Python traceback. Any idea of what is going wrong?

2 3

[Query] Possible to control tool panel size programmatically?
by leeyang+chimerax＠gmail.com 03 May '24

03 May '24

Hi, Not a feature request but a query. Is there currently a way to change tool panel sizes with a command, either in absolute terms or as a fraction of another parameter value? Cheers, Yang

3 4

Installing ChimeraX on Ubuntu 24.04 LTS
by mborgnia＠gmail.com 02 May '24

02 May '24

Hi all, I got a shiny new machine with Ubuntu 24.04 LTS, unfortunately the regular repositories do not include libffi7 and that causes a failure when installing the 22.04 package. I have also tried to run the generic Linux 64 bit version but fails to load because the libffi.so.6 file is not found. Any ideas on how to proceed? Thanks Mario J. Borgnia

3 6

Using chimerax library code outside of the GUI
by Artie Kushner 02 May '24

02 May '24

Hi, I apologize sincerely since I imagine this comes up often on the mailing list. I'm basically wondering if it's possible to import just the `core` functionality from a chimerax installation into a custom python environment and bypass the GUI and the binary completely. Example: I don't think it matters whether it's linux, mac, or source build, but let's say i installed a clean chimerax via my package manager (`yay i chimerax`). It's at `/opt/chimerax` and looks like this: (venv) ᢹ ritual.rtviii[ /opt/chimerax ] ls -la total 24 drwxr-xr-x 6 root root 4096 May 1 16:08 . drwxr-xr-x 10 root root 4096 May 1 16:58 .. drwxr-xr-x 4 root root 4096 May 1 16:51 bin drwxr-xr-x 8 root root 4096 May 1 16:51 include drwxr-xr-x 4 root root 4096 May 1 16:51 lib drwxr-xr-x 6 root root 4096 May 1 16:51 share If I launch `chimerax` at the command line, i get a functional GUI etc. It works. I create a fresh custom `virtualenv` with the same python that this chimerax ships: virtualenv --python='/opt/chimerax/bin/python3.11' venv Then i do something ugly in the name of science: i symlink the chimerax folder from the installation into my virtualenv: ln -s /opt/chimerax/lib/python3.11/site-packages/chimerax /home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax i also tried: for P in $(ls /opt/chimerax/lib/python3.11/site-packages/); do ln -s /opt/chimerax/lib/python3.11/site-packages/$P /home/rtviii/dev/try_chimerax/ venv/lib/python3.11/site-packages/$P; done This enables me to import chimerax modules into my python code that uses this virtualenv: ```/home/rtviii/dev/try_chimerax/test.py from chimerax.core.commands import run from chimerax.core.session import Session import chimerax.mmcif.mmcif as mmcif s = Session("Hi") print(s) run(s,"open 1ubq.cif") ``` However, this is where i'm struggling a little to use any actual functionality (especially interested in cutting, merging structures and operations treating density maps and mmcif structures) because the Session wouldn't initialize well: ``` <chimerax.core.session.Session object at 0x70472673b5d0> NOTE: Traceback (most recent call last): File "/home/rtviii/dev/try_chimerax/test.py", line 9, in <module> run(s,"open 1ubq.cif") File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2849, in run _compute_available_commands(session) File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands ts.register_available_commands(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute'register_available_commands' BUG: AttributeError: 'NoneType' object has no attribute'register_available_commands' File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands ts.register_available_commands(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ ``` I had some success with a similar approach in PyMol in this regard, but can't quite get this to work in ChimeraX. I really appreciate any advice for achieving this scripting decoupling from GUI/binary if that's possible at all: - either how to "pull in" ChimeraX library code properly (i realize mine is an ugly hack) - how to use library code otherwise - how to bypass the dependence of a lot of commands on the Session object or how to initialize it outside of the gui properly: an example of how to use selections to open a local density map and perform a smoothing, for example. Kindest regards and huge thanks for the monumental application. Artem, UBC Vancouver

2 1

Problem visualizing hydrogen bonds during a trajectory
by Ute Roehrig 02 May '24

02 May '24

Hello, I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands: alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe However, this does not work as expected. Could you please help me with this issue? Thank you, Ute

2 2

Visualizing PAE contact lines between more than two peptides
by David S. Fay 30 Apr '24

30 Apr '24

Greetings, Was wondering if it’s possible to simultaneously display PAE contact lines for more than two peptides? For example, all contacts between A and B AND B and C etc. Couldn’t find anything on it and have already made the obvious attempts such as "alphafold contacts /A to /C AND /B to /C distance 6” Thanks! David

2 2

Schematic
by Das, Abhinaba 30 Apr '24

30 Apr '24

Hi all, I don’t think it is possible to draw this kind of schematic representation (panel b) in ChimeraX, is it? [cid:image001.png@01DA9A41.C6E2E040] Thanks, Abhi

3 2

Alphafold predicton using ChimeraX
by Chang, Jufang 29 Apr '24

29 Apr '24

Dear Sir, When I tried to use alphafold prediction with ChimeraX, I got this error message. I alreday download the latest version 1.7.1 (2024-01-23). But I still got the same error message. Could you please suggest me what to do the next to fix this? Thank you Ju-Fang AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

running AlphaFold predictions in ChimeraX
by Elaine Meng 29 Apr '24

29 Apr '24

> On Apr 29, 2024, at 9:31 AM, Chang, Jufang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Greg > > Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? > > Thank you > > Ju-Fang Hello Ju-Fang, As Greg said, you should use the address chimerax-users(a)cgl.ucsf.edu for ChimeraX questions, not chimera-users(a)cgl.ucsf.edu which is for Chimera, and put some description of the current issue in the email subject line. If you get an error running the AlphaFold prediction in ChimeraX and you think it is a bug, please use ChimeraX menu Help... Report a Bug and include a description and your email address. As far as I knew it was working, so we wouldn't know what the problem is for you without more information. Also here are some common issues and limitations of running these predictions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#caveats> 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

2 3

Unroll radius?
by Ricardo Righetto 29 Apr '24

29 Apr '24

Hi, We've been using the 'volume unroll' command on a cylindrical structure, and while we do get some very decent results with the defaults, we want to do a systematic comparison with values entered manually for the inner and outer radius. Specifically, I'd like to know if I can get ChimeraX to report what minimum and maximum radii it is currently using for unrolling the volume? Currently, all I get in the reply log is this: volume unroll #1 Opened unrolled SPA_density.mrc as #2, grid size 68,697,492, pixel 1.22,1.2,1.2, shown at step 1, values float32 https://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/UsersGuide/midas/v… From the help here it says: > (...) and inner and outer radii *r1* and *r2* (defaults are 90% of the > smallest radius and 110% of the largest radius of the displayed isosurface, > respectively, given the cylinder center and axis direction). Since this is a high-resolution cryo-EM map with many intricate features, it's hard to visually find exactly what are the smallest and largest radii currently displayed at the isosurface. So we'd like to know what ChimeraX is finding by itself and compare it to our measurements. Any tips are appreciated. Thank you! -- Ricardo Diogo Righetto

2 4

Glb files
by Rowe-Magnus, Dean 28 Apr '24

28 Apr '24

Hello, Can you please tell me how to save a .glb file as a .pdb so that I can use Matchmaker to align the structures? Thank you, Dean

2 1

How to show van der Waals surface
by 我就要柠乐 26 Apr '24

26 Apr '24

Dear Sir/Madam         Recently, I have been using ChimeraX for graphical analysis, and I find the software to be very user-friendly and efficient. I am currently facing a challenge where I want to display the van der Waals surface of a residue, similar to this illustration（https://doi.org/10.1038/s41467-022-31526-7）. However, I am not quite sure how to write the command correctly. I have looked up the commands on the official website and tried using these two:surface #1:230； surface style mesh. The bottom is open （the rad circle）, but I would like to have a complete van der Waals surface with closed openings, similar to what is typically seen in the literature. I would appreciate your assistance. Thank you！                                                                                                                       yours  sincerely                                                                                                                       yiwen 我就要柠乐 790639436(a)qq.com  

2 2

Question about visualisation of DNA structure
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X users, I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)? Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ? Many thanks in advance ! Enrico

2 7

Add options to snapshot command
by Jaremko, Matt Joseph 26 Apr '24

26 Apr '24

Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

3 3

palette command
by Cairns, Claudia Anna 26 Apr '24

26 Apr '24

Dear sir or madam, I try to apply the palette command to change the color range of the mlp command. Unfortunatelly i always get an error. For "palette rainbow" for example I get: rainbow Unknown command: palette rainbow Can you please help me? Sincerely, Claudia Cairns M.Sc. (Biotechnology) Department 'Applied and Molecular Microbiology' Institute of Biotechnology - TIB 4/4-1 Technische Universität Berlin Gustav-Meyer-Allee 25 D-13355 Berlin Phone: +49-(0)30-314-72827 E-mail: c.feurstein(a)tu-berlin.de<mailto:carsten.pohl@tu-berlin.de> Web: <http://www.mikrobiologie.tu-berlin.de> https://www.tu.berlin/mikrobiologie/

2 1

Reconstruction of missed loop fragments
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X user! I am preparing a model of GPCR protein for the molecular dynamics simulation. In this structure there is a loop fragment of 10-20 residues which is missed. Is it possible to reconstruct it (e.g. based on the sequence information or alternatively just add manually the missing fragment) using some tool of Chimera-X e.g. combining with the bond command ? Many thanks in advance ! Enrico

2 7

Greek characters
by Marta Martinez 25 Apr '24

25 Apr '24

Hi guys, I just downloaded a pdb file from AlphaFold DB (AF-P69905-F1-model_v4.pdb). After modifying it with ChimeraX (version 1.6.1 (2023-05-09)) I've saved the modified atomic structure as a cif file. The original pdb file contains this line: COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; After saving the file as cif format ALPHA is not longer a string but a GREEK character: _entity.pdbx_description "hemoglobin subunit α" Is there any flag in the save command that disables this conversion from plain ASCII to UTF-8? Thank you very much for the answer in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

2 1

atom serial_number is inconsistent with PDB serial numbers in multi-chain structure
by Daniel David Richman 25 Apr '24

25 Apr '24

Hi all, I’ve been debugging an off-by one error in a ChimeraX script I’m working on, which I’ve traced to a apparent inconsistency between the serial_number reported by ChimeraX for an atom and the actual serial number of that atom read/written in PDB format. To reproduce: open 5MJ7 select #1/B:6@CA info atoms sel attribute serial_number ==> atom id /B:6@CA serial_number 2548 but the correct serial number for this atom in 5MJ7.pdb is 2549. Maybe this is because the TER record for chain A takes up one serial number in the PDB file, but ChimeraX doesn’t include it as a numbered atom? Regardless, how can I query ChimeraX for the actual serial number that will be written if I write out a PDB file? Thanks, Daniel

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How to make an MD template for ISOLDE?
by Guillaume Gaullier 25 Apr '24

25 Apr '24

Hi Tristan and chimerax-users, Some time ago I asked the list about modeling PTM and got several helpful answer, including this one: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… Now, I am working on a structure containing chlorophyll A molecules (residue code CLA) and realized that it won’t work for MDFF in ISOLDE because there is no MD template for it. After trying to manually fit one of these molecules rigidly, I concluded that I would rather spend the rest of the month learning how to make an MD template for it (than next month painstakingly fitting every single molecule manually rigidly). From the message linked above, I think this should be doable because this time it is not a covalent modification on an otherwise parameterized residue, but simply a new ligand (ok, maybe the coordinated Mg2+ makes it a bit more complicated?). I looked up ANTECHAMBER, and also some documentation from OpenMM, but that got me nowhere, mostly because I have little clue what the task really entails. My guess is that I need some program to take the CLA residue in PDB or mmCIF format (which I can easily save from a previous PDB entry) and write out an OpenMM XML file like the one you sent me back then for KCX. Is this correct? The ANTECHAMBER documentation mentions many programs and formats, and I got totally confused. If you have time to elaborate a bit on the specific practical steps to take (including how to supply the final XML file to ISOLDE), that would be super helpful! I can do with pointers to documentation, not afraid to read, but I need help getting oriented. Thank you in advance! Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Realsense issues
by Casey Eubanks 24 Apr '24

24 Apr '24

Hey guys, You all helped me a week or so ago getting the Realsense package updated to the new version of chimerax, which I can now download so thats great! But I am now having an issue with running its command "Realsense on" I receive the following errors attached to this email It is having errors processing the trigger and it says it cant resolve the requests. Let me know if I am doing anything wrong or need to make any changes! Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image001.png@01DA9660.03D4DE80]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 2

Finding unmodeled blobs in a map
by Guillaume Gaullier 24 Apr '24

24 Apr '24

Hello, With `volume zone` I can show the parts of a map close to an atomic model. Is there a way to do the opposite, i.e. show only the parts of a map that don’t enclose any atoms? This would be already very helpful only as a visualization. But even better would be a way to build a list of markers at the centroids of such unmodeled blobs, to easily navigate to them. Or maybe this is too narrow in scope and better left to ISOLDE? (Sorry Tristan… more feature suggestions…). Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 2

Adding missing atoms of the DNA structure
by Enrico Martinez 24 Apr '24

24 Apr '24

Dear Chimera-X users I am preparing the structure of the protein-DNA complex for molecular dynamics simulation with Amber. This is the original pdb: https://www.rcsb.org/structure/5FKW When I try to parametrize it the tleap shows the following error because of the absence of some atoms from the phosphate: FATAL: Atom .R<DG5 733>.A<P 32> does not have a type. FATAL: Atom .R<DG5 733>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 733>.A<OP2 34> does not have a type. FATAL: Atom .R<DG5 758>.A<P 32> does not have a type. FATAL: Atom .R<DG5 758>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 758>.A<OP2 34> does not have a type. Would it be possible to use some commands of the Chimera-X to automatically repair this part of the DNA by adding missing atoms ? Thank you in advance ! Enrico

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Cutting out an asymmetric unit from the map
by Das, Abhinaba 23 Apr '24

23 Apr '24

Hi! I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density. Thanks in advance for any guidance. Abhi

3 2

Lighting options in ChimeraX
by Elaine Meng 22 Apr '24

22 Apr '24

> On Apr 20, 2024, at 7:36 PM, Friedman, Simon <friedmans(a)umkc.edu> wrote: > > I am working on mol graphics for a figure. I'm using both chimera-x and chimera. I'm trying to figure out if chimera-x has a set of functionality that chimera has. Specifically in chimera I was able to move light sources around, change intensity, shinyness etc. Also I was able to use ray tracing in the output. In chimera-x I can't find any menu for moving light sources around etc. One very cool thing that is there is the 'soft' lighting option which gives a very cool surface to the carbon atoms. So I was wondering if there were more options for messing with lighting etc in chimera-x? > Thank you! > > Cheers, > Simon > > Simon H. Friedman, Ph.D. > UM Curators' Distinguished Professor > Division of Pharmacology & Pharmaceutical Sciences > University of Missouri, Kansas City Hey Simon! ChimeraX does not have ray-tracing, but as you discovered with the ChimeraX "soft" lighting (sugar cube icon in the toolbar), it does have ambient-occlusion lighting simulated by multiple multidirectional light sources, which Chimera does not have. The rest of this description pertains to ChimeraX: When you try the different lighting icons in the toolbar, the corresponding command is shown in the Log. So that should help you learn some of the common options. However, there are lots more options available with the commands than are represented by toolbar icons. (1) the "lighting" command has the presets including soft, but also options for intensities, colors and directions of the directional lights (key light and fill light), depth cueing, and shadows, among many other things. There is no GUI for changing the direction interactively, however. See the "lighting" manpage and many options explained therein. It also shows pictures of the relevant icons from the toolbar. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> (2) the "graphics" command has options for background color, silhouette edges (the outlines that are usually black), and triangulation fineness of atom/bond/ribbon representations, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> (3) the "material" command has control over shininess of objects <https://rbvi.ucsf.edu/chimerax/docs/user/commands/material.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

1 0

Running AlphaFold through Chimerax vs. Colab directly
by Coyle, Maxwell C 22 Apr '24

22 Apr '24

Hello! I’ve been predicting structures recently using the AlphaFold tool through ChimeraX (which directs to the alphafold21_predict_colab.ipynb notebook), but I’ve noticed I get often quite different results when I run the same prediction through the AlphaFold.ipynb notebook directly in Colab. I was wondering if anybody could point me to the major differences between these two implementations? Are they searching different libraries to generate a multiple sequence alignment? Are they using different numbers of iterations or energy minimization strategies? Thanks for any guidance, Max Max Coyle, PhD Postdoctoral Fellow, Bellono Lab Dept of Molecular and Cellular Biology Harvard University mcoyle(a)fas.harvard.edu

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