- ChimeraX-users - RBVI Mailing Lists

seeking AlphaFold advice
by Elaine Meng 30 Jul '24

30 Jul '24

Hi David, Please send questions to the chimerax-users address CC'd here instead of to me individually. I am not an AlphaFold expert, whereas maybe others on the list can answer your questions. I removed your link because I didn't know if you were willing to share it publicly. If so, please repost to the group (chimerax-users address CC'd here). Best, 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 Jul 30, 2024, at 6:26 AM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Thanks for that information Elaine. That is my take as well, but I know much less about these things… > > On a slightly different note, I really wish there was an alphafold “best practices” tutorial or methods paper. Mainly I’m focused on protein-protein interactions, which is something I think many people are interested in. I gave a talk to my department recently, where I tried to do some of this. But because this isn’t my area, I rather feel like this is a case of the slightly blind leading the even-more blind. Still, I’ve attached a link to a google folder that contains my talk. I’d love to get feedback on this from experts in the field, such as folks at ChimeraX. > > And one last question, which you might have an opinion about. Is AF3 any good at predicted changes in structure with amino acid substitutions? I know that AF2 was not, but given that AF3 includes secondary modifications, it would seem like this capability should be improved? Especially if it’s relying less on MSAs. For that matter, do the folks at ChimeraX have an opinion about how AF3 alters structure and interactions based on modifications like phosphorylation? > > Thanks, > > David

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Hide axis indicator
by Hantz, Eric 30 Jul '24

30 Jul '24

Hello, I am using ChimeraX 1.8 macOS, and I am having trouble finding a way to hide the axes indicator. I am trying to make a figure of a ligand bound protein structure with the electron density shown for the ligand. The best I can have been able to do is make the axes indicator slightly transparent but it is still visible. Thanks, Eric

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Re: Answer to question regarding Consurf and ChimeraX
by Elaine Meng 29 Jul '24

29 Jul '24

Hi David, There is no option to call the ConSurf web service from inside ChimeraX (or Chimera), I just meant to ask whether you could display the output in ChimeraX. I didn't know the recent version of the ConSurf server provided ChimeraX sessions, so that is helpful, thanks! You would have to talk to the ConSurf website developers about what information they put into the session. However, I would not expect it to have any Alphafold information (pLDDT or PAE values). It probably just has whatever atomic coordinates you uploaded (if that's how you input the structure), or atomic coordinates straight from the PDB. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2024, at 8:04 PM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Hi Elaine, > > I was able to open the ConSurf .cxs files using ChimeraX, which were part of the Consurf download. I have tried using ConSurf through Chimera or ChimeraX yet. I’ve attached an example image I recently obtained using ChimeraX. One limitation I haven’t worked is how to display PAE contacts between peptides when using this ConSurf file in ChimeraX. I can do it with AF2/3 files – no problem, but not with the ConSurf files. Also, the .cxs files don't seem to work for other ChimeraX functions, such as: hide @@bfactor<50 ribbon. It’s also unfortunate that ConSurf doesn’t allow you to visualize conservation for more than one of the two peptide chains, at least as far as I can tell. But it’s still quite useful. > > If you have any additional hints I’d be glad to try them. > > David > > > > <Screenshot 2024-07-26 at 8.54.04 PM.png> >> On Jul 26, 2024, at 3:11 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi David, >> Thanks for the info about the ConSurf website. Did you ever use the ConSurf website output in ChimeraX or were all the outputs only suitable for Chimera (which was my experience)? >> >> Some other notes, in case you or others didn't know... >> >> (1) ChimeraX also plots PAE data from AlphaFold2 or AlphaFold3 >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> >> >> example command: >> alphafold fetch LDLR_HUMAN pae true >> >> screenshot of result: >> <Screen Shot 2024-07-26 at 2.10.24 PM.png> >> >> (2) ChimeraX can convert mmCIF to PDB, i.e. you could just open the mmCIF file and then save the structure as PDB. Can be done with the File menu or with the commands "open" and "save": >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> >> >> Elaine >> >>> On Jul 26, 2024, at 1:54 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Real quick followup for those who might be interested. >>> >>> I did contact ConSurf. They suggested using a different browser and clearing the cache. I did both and it now works but only on Chrome and NOT on Safari (for those using Macs). This isn’t the first time I’ve had problems with Safari. ConSurf is helpful for looking at conservation of a protein sequence and/or a 3D structure. >>> >>> Incidentally, for converting cif to pdb, which is necessary for ConSurf, this site worked well. >>> https://project-gemmi.github.io/wasm/convert/cif2pdb.html >>> >>> Also, some may be interested in using this site to generate AF2-like red/blue PAE diagrams as well as creating spreadsheets of predicted peptide interactions from AF3. >>> https://predictomes.org/tools/af3/ >>> >>> David >>> >>>> On Jul 25, 2024, at 9:42 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> ◆ This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources. >>>> >>>> >>>> Hi David, >>>> Did you try asking the Consurf developers? There is a "contact us" link on their website: >>>> >>>> <https://consurf.tau.ac.il/consurf_contact.php> >>>> >>>> I haven't used this web service recently. I have only used its outputs in Chimera so far (never ChimeraX). >>>> >>>> If I go to a page for precalculated results there is a "Chimera" download that gives a Chimera session (.py file), e.g. >>>> >>>> <https://consurfdb.tau.ac.il/main_output.php?pdb_ID=2GBP&view_chain=A&unique…> >>>> >>>> I tried downloading that just now, and it works in Chimera. In Chimera you can use File... Export Scene... and export a .py file that you can open with ChimeraX. Only the ribbon and carbon atoms are colored by the Consurf values, however, not the heteroatoms. >>>> >>>> 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 Jul 24, 2024, at 8:08 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) >>>>> >>>>> Thanks in advance! >>>>> >>>>> David >>>> >>> >>> _______________________________________________ >>> 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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Doubt about volume cropping
by Leyre Marin Arraiza 29 Jul '24

29 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding 3D volume visualization and cropping in ChimeraX. I have a big 3D density map which includes the densities for several models of different proteins. To facilitate visualization and model building, I would like to crop the density map, so that it includes only two of the models. Is it possible to crop my density map around those models, to make it a bit smaller and more focused on the areas of interest? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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ChimeraX adjacent question about ConSurf
by David S. Fay 26 Jul '24

26 Jul '24

Hi, I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) Thanks in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming davidfay(a)uwyo.edu

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Question about Creating/Displaying Vectors
by John Watters 25 Jul '24

25 Jul '24

Hi All, I was wondering if anyone had any advice on how to make figures where vectors show the difference in the RMSD of the alpha carbons like in A/C here in ChimeraX: [https://iiif.elifesciences.org/lax/51898%2Felife-51898-fig3-v2.tif/full/617…] From this paper: https://elifesciences.org/articles/51898 [https://elifesciences.org/assets/images/social/icon-600x600@1.52e87ee6.png]<https://elifesciences.org/articles/51898> Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing<https://elifesciences.org/articles/51898> Chemical modifications near the tRNA anticodon and specific mRNA–tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains. elifesciences.org

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Re: combining and splitting chains
by Elaine Meng 25 Jul '24

25 Jul '24

Hi Dmitry, You can do the combining into one model with "combine" and the splitting into multiple models with "split", see links in my previous message. The "split" command can use residue ranges (not just chain IDs) so you can split it however you want even if it is one chain. However, I don't know if it makes sense to make it all one chain, but I think Eric already explained that part in his reply. The "changechains" command can change the chain ID, and "rename" can change the model name and ID: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine > On Jul 25, 2024, at 9:05 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > Thank you for your answer. > You were right. I meant to combine chains inside 1 model so that there would be only 1 model with 1 chain (instead of multiple). > Can we rename all of them to 1? > And vice versa — when there is one model, and one wants to split it into domains (chains)? > Any ideas? > Thank you. > Kind regards, > Dmitry > > Ps. Sorry, I can not send the emails with illustrations to ChimeraX somehow.From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: 22 July 2024 18:10 > To: Dmitry Semchonok <semchonok(a)gmail.com> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] combining and splitting chains > Hi Dmitry, > I thought you meant combining multiple chains into a single chain. However, if you instead meant combining chains that are in different models into a single model (still with multiple chains), see command "combine": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > Then if these chains have different chain IDs, it is easy to split that single model into multiple models again, one for each chain, with "split": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> > > Regards, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 20, 2024, at 3:50 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hello Eric, > > Thank you for your answer. > > Following up combining and splitting chains topic I would like to specify more details. > > My question is connected to modelangelo output where one gets the separate chains. I would like to combine those chains in one structure. > > But maybe later I may need to divide the complete structure on chains again. > > Kind regards, > > DmitryFrom: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Sent: 17 July 2024 19:26 > > To: Dmitry Semchonok <semchonok(a)gmail.com> > > Cc: ChimeraX <chimerax-users(a)cgl.ucsf.edu> > > Subject: Re: [chimerax-users] combining and splitting chains > > > > Hi Dmitry, > > You don't say why you want to combine/split these chains, so there might be more direct way to accomplish whatever your ultimate goal is than my answers below, if we knew what your goal was. > > You combine chains by using the 'bond' command (or Build Structure tool) to form the C→N bond (or O3'→P bond for nucleic acids) between the chains. ChimeraX will combine them into a single chain. > > Splitting chains is uglier because ChimeraX knows that the residues in a chain form a chain even if you delete connecting bonds or even entire residues. The recipe would be to open multiple copies of your model. In the first copy, in the chain you want to split delete everything but the first "segment" you want split off. In the second copy delete everything but the second segment (and all other chains if there are any). So on and so forth. Then use the "combine" command to combine the models into one. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > > >> On Jul 17, 2024, at 9:33 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear colleagues, > >> I have a lot of chains that I want to combine just in 1. > >> How to do that? > >> And vice versa – I have 1 chain, and I want to split it into several. > >> Thank you in advance, > >> Kind regards, > >> Dmitry

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Re: ChimeraX-SASA mismatch with contiguous sequences
by Elaine Meng 24 Jul '24

24 Jul '24

Dear Suhas, I hope your week is great as well, and we're glad you like ChimeraX! We recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless they include private data. That way others can also answer, or benefit from the answers. In this case, it is explained in the "measure sasa" help. Please see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> The command measures the surface area *enclosing* the specified atoms. That is different than the surface area of those atoms in the context of the larger structure. So when you give two commands measuring two parts you also get more surface that goes around the ends of those parts. If you wanted the SASA in the context of the whole protein or whole chain, you would have to do it differently. As explained in the help link above, if you want to measure the SASA of those parts in the context of the whole protein chain's surface, it would instead be something like measure sasa /A sum /A:1-10 measure sasa /A sum /A:11-20 measure sasa /A sum /A:1-20 The Log gives: measure sasa /A sum /A:1-10Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-10 (66 atoms) of /A (2615 atoms) = 1143 measure sasa /A sum /A:11-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:11-20 (80 atoms) of /A (2615 atoms) = 427.09 measure sasa /A sum /A:1-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-20 (146 atoms) of /A (2615 atoms) = 1570.1 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 Jul 23, 2024, at 11:59 PM, Suhas Srinivasan <suhas.srinivasan(a)stanford.edu> wrote: > > Dear Dr. Meng, > > Hope you are having a great week! > > Thank you for developing and maintaining ChimeraX as an essential analytical software for the community. > > We had a query since we noticed a discrepancy in the way SASA is reported. > If you were to consider the AlphaFold database structure for PCBP1 (Q15365) and perform the below SASA measurements, we noticed that: > SASA(1 to 10) + SASA(11 to 20) ≠ SASA(1 to 20) > > measure sasa /A:1-10 > Solvent accessible area for /A:1-10 (66 atoms) = 1385.3 > measure sasa /A:11-20 > Solvent accessible area for /A:11-20 (80 atoms) = 1632.6 > measure sasa /A:1-20 > Solvent accessible area for /A:1-20 (146 atoms) = 2850.8 > > There is a difference of ~167 sq. A. > It would be very helpful to understand why such a large difference exists when considering contiguous sequences of atoms/residues. > > ChimeraX-1.8 > macOS-14.5 (Intel) > > Thank you for your consideration. > > Kind regards, > Suhas Srinivasan

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Re: [Chimera-users] column selection: chimera vs chimeraX
by Eric Pettersen 23 Jul '24

23 Jul '24

Hi Mike, There wasn’t, but I just added code to do it. In tomorrow’s daily build (well, the next daily build that works :-) ) the alignment viewer’s context menu will have an “Expand Selection to Columns” entry that will do this. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Jul 22, 2024, at 9:01 AM, 7mkf via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi there, > > I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? > > Many thanks, > Mike > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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saving modifications
by Claudio Andres Aguilar Pena 23 Jul '24

23 Jul '24

Dear ChimeraX team, First of all, many thanks for the app, it’s really wonderful!. I have a question regarding one feature I would like to have and maybe it’s possible to do but I just don’t know how. I have a PDB of the structure of an enzyme that has 5 different domains: I can select the aa of each domain and give each domain a color. This is very useful for me when comparing structure predictions of the enzyme and see what happens when making mutations in the primary structure. My problem is that I cannot save the PDB with the colors for each domain, so I have to select and assign the colors every time, or leave the app and the PDB permanently open, which is not very convenient. Is there a way to save the PDB with the modifications I made? Many thanks for your help. Best, Claudio Dr. Claudio Aguilar, PhD Virologisches Institut Universität Zürich Vetsuisse Fakultät Winterthurerstrasse 266a CH-8057 Zürich Switzerland phone: +41446358712 Fax: +41446358911

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