- ChimeraX-users - RBVI Mailing Lists

Assistance Required: Visualizing Complete Amino Acid Residue with Cartoon Transparency in ChimeraX
by Amandeep Sharma (P24BB0001) 19 Aug '24

19 Aug '24

Dear ChimeraX users, I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result. To provide context and illustrate the issue, I am enclosing images of the current visualization: - *Image 1:* Shows the current state where part of the residue is obscured by the cartoon structure. - *Image 2:* Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms. I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency. Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX. Best regards, Amandeep -- Amandeep Sharma PhD Student (2024-25) Dept. of Bioscience & Bioengineering Indian Institute of Technology Jodhpur Karwar 342037, Rajasthan

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Alligning a trajectory
by ygilron＠asu.edu 19 Aug '24

19 Aug '24

Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai

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2D labels colored by chain color
by NG, Cheukhei Jackie [Student] 19 Aug '24

19 Aug '24

Dear sir/madam, I am trying to generate publication-quality images with chimeraX with appropriate 2D labels. 1. Is there a variable I could use to represent the coloring of my current chain so i can apply in the command where the selection is multiple chains: label sel color (the variable)? 2. is the an offset parameter or any relevant parameters in the 2D label command that are recommended for publication use? Thank you very much for your time. Thanks, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Feature of chimera
by Arpita Nandy 19 Aug '24

19 Aug '24

Hi, I am a PhD student from Germany and would like to make a figure where I can highlight specific proteins of interest in the mitoribosome complex of yeast. Could you please assist me to use ChimeraX in this context. Best regards Arpita Nandy

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Usage and Distribution of ChimeraX at our Upcoming Max Planck Institute Summer School
by SantaLucia, Daniel 15 Aug '24

15 Aug '24

Hello ChimeraX team, My name is Dan SantaLucia; I'm a research scientist working under Prof. Frank Neese and Prof. Serena DeBeer at the Max Planck Institute for Chemical Energy Conversion. One thing we do every year is to organize a summer school for students from all over the world, where they get to learn in-depth about many different spectroscopic techniques as well as quantum chemical calculations to help them in their interpretations of these datasets. You can find more information here, if you're curious: https://summerschool.cec.mpg.de/en/home thing that would be really nice would be to offer students the ability to use ChimeraX alongside our tutorial/practical sessions. We use ORCA to do calculations (considering, of course, that Frank invented it), and we've found that ChimeraX has a lot of really nice features that would be perfect for helping the students to learn. What I wanted to ask was this: do we have permission to distribute the download files at: https://www.rbvi.ucsf.edu/chimerax/download.html to the students? They would be distributed on flash drives that we give to the students, and we would distribute the Windows, Mac, and Linux versions so that we could cover all users. The internet connection is not the best, unfortunately, at our venue, which is why they can't just go to the link to download it themselves. To be clear: this is a non-commercial use event, where we simply have international students coming to attend the summer school, and this is an event that is for learning purposes only. Nonetheless, I want to have your explicit permission for distribution of ChimeraX to the students as well as your permission for them to use your software at our summer school? Thanks so much, and looking forward to hearing back from you, -Dan [1668779311055] [1668779979115] Dr. Daniel J. SantaLucia MPI-KoFo/CEC Joint Workspace Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany Tel.: +49 208 306 3724

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problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

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ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

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AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

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Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

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Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

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problem for the PDB deposition
by Yanhe Zhao 07 Aug '24

07 Aug '24

Dear ChimeraX community and developer, I am trying to deposit my map with model. I save the model from pdb to cif in ChimeraX because of large amount of atoms, then got error as "Missing '_entity_poly.pdbx_strand_id' item. I tired to use pymol to open my pdb and save it as cif by 'Export Molecule', in which I just use the default options. I checked the saved cif in ChimeraX, which is weird since it couldn't be show in cartoon style. Is there any easy to handle this in ChimeraX or any option should be used in the 'Export Molecule' in Pymol? Thanks and cheers, Yanhe

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Inverted fit in map ?
by GOVAERTS Cédric 07 Aug '24

07 Aug '24

Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Question regarding per-Residue RMSD
by Zimiao Meng 07 Aug '24

07 Aug '24

Dear Developers/Researchers of ChimeraX, I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script? Best, Zimiao

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Looking for scale
by David S. Fay 07 Aug '24

07 Aug '24

Hi, Does anyone know if a reference-type PAE bar exists for the ChimeraX PAE plot when using the Rainbow (orange/yellow/blue) selection? Something similar to what AF provides for the (green) scale (below) or the electro-charge (blue/white/red) maps? Rainbow provides a nice visual range, but I couldn't find an associated score reference. [cid:7001d3eb-43d0-4009-9596-6843ea44695a@namprd05.prod.outlook.com] Thanks, David

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ChimeraX website not accessible from time to time
by Roden Deng Luo 07 Aug '24

07 Aug '24

Hi, This has happened quite some times in the last few months. I realized just now that I could not access https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/logger.html. I then checked the following, and all were not working. Is this my own problem or a server-side issue? Is there an offline developer documentation (PDF or HTML)? https://www.cgl.ucsf.edu/chimerax/docs/user/commands/log.html https://www.cgl.ucsf.edu/chimerax/download.html https://www.cgl.ucsf.edu/chimerax/docs/licensing.html Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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PhenixUI Installation Errors
by Caballero Silva, Guillermo 06 Aug '24

06 Aug '24

Good afternoon, I am a current postdoctoral fellow working primarily with low resolution (4-6A) CryoEM Data/Models and recently discovered the "Local EM Fitting Tool" described in https://doi.org/10.1101/2024.05.16.594509 which I believe will help me overcome some of the issues I am currently experiencing in model docking/building. I am currently running ChimeraX version 1.5 and Phenix-1.20.1-4487 and have been trying to install PhenixUI from ChimeraX "More Tools" but have not been able to. I have tried installing older version of PhenixUI but was only able to install PhenixUI version 1.0.5. When I try to upgrade to the current version I am received with the following message: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\gcaballe\downloads\chimerax_phenixui-1.2.2-py3-none-any.whl Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\users\gcaballe\documents\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.2.2) (2.0) ERROR: Could not find a version that satisfies the requirement ChimeraX-Map~=1.1.3 (from chimerax-phenixui) (from versions: none) ERROR: No matching distribution found for ChimeraX-Map~=1.1.3 [notice] A new release of pip available: 22.2.2 -> 24.2 [notice] To update, run: C:\Users\gcaballe\Documents\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip It is my understanding that I need to install "ChimeraX-Map~=1.1.3" but cannot find how/where to do so. My current OS is Windows x64. Is it possible to install Local EM Fitting with my current set up or do I need to do any changes modifications. Please let me know if there is any more information I can provide and thank you in advance for your help and support. Kind regards, Guillermo Caballero Silva Postdoctoral Fellow Amgen Canada [cid:image001.png@01DAE4FC.105C31E0]

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Doubt about "contacts" command in ChimeraX
by Manuel Ospina 05 Aug '24

05 Aug '24

Good evening, I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this? Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts? Any help is appreciated. Best regards, Manuel

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Silhoutte
by Shubhangi Agarwal 05 Aug '24

05 Aug '24

Dear developers, I am trying to outline surfacerepresentation of my protein structure with the silhouette feature but it gives me black dashes along rest of the surface which I don’t want, how can I just use the black borderline feature for my surface and protein? Figure attached below. Thank you Shubhangi [cid:922B93FD-C686-4CED-8281-EFF2FAFC08D2]

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2D PAE plot with colored PAE domains
by David S. Fay 05 Aug '24

05 Aug '24

Hi All, Was trying to get the ChimeraX 2D PAE plot to display the colored PAE domains consistent with the ribbon diagram. The button “Color PAE Domains” colors the ribbon diagram by coherent domains, but the 2D plot is still colored by PAE (error). The Meng et al., 2023 has nice examples of this (e.g., 1f) coloring. Thanks in advance! David

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save images
by Aritz Roa Eguiara 02 Aug '24

02 Aug '24

Dear Sir or Madam, I am trying to make a default .cxc file that I can use to automatically save the view for publication. I am using the following: save /path/image.tiff pixelSize 0.05 supersample 4 This turned out to give me the best files for most cases, but depending on the zoom I get different file sizes. Is there any way to have a standard command that gives me high quality images and that always have the same dimensions regardless of the zoom? I understand that the issue comes from the different pixel size of the zoom and that I am specifying a pixel size on the command, but when trying other alternatives I have not been successful to get proper images... All the best, Aritz

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August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, 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

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PDB search in ChimeraX
by Enrico Martinez 01 Aug '24

01 Aug '24

Dear ChimeraX users, I have a pdb structure of membrane protein without any information about it. Is it possible to use some chimera-X tool to identify the name of this protein and find its pdb code in pdb database ? Many thanks in advance Enrico

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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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