May 2024 - ChimeraX-users - RBVI Mailing Lists

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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