May 2024 - ChimeraX-users - RBVI Mailing Lists

Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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"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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