- ChimeraX-users - RBVI Mailing Lists

bonding Question
by Noriega, Heather 09 Feb '22

09 Feb '22

Hello, I hope you are well. I have a quick question about the bond command. I attached the pdb file I have been using to try and learn this command. I am having a hard time figuring out how I should write it on the command line. If I want to create a bond between residue Lys76 from the antibody and the Oxygen #2 from my polymer, how would I write it on the command line? bond :lys76:O2 I have read the section in the manual but I think I am misunderstanding something, it keeps giving me a mangled atom specifier. Also, I figured out the problem from my last question/email about the volume in my viral capsid. :) Thank you for your help on that one Elaine. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Pseudo bonds of missing structure in cartoon style
by Wout Oosterheert 09 Feb '22

09 Feb '22

Dear ChimeraX team, I’m making figures of a protein structure that has 4 residues missing in a flexible region. When I show the atoms as “style stick”, I can see a dashed pseudo bond between the two residues that connect the missing segment. However, when I “show cartoons” of the same structure, the dashed line disappears and the pseudo bond is no longer visible. Would you have any suggestions on what to change to make the missing structure appear as a dashed line when the model is shown in cartoon style? Of interest, in a similar structure where 3 instead of 4 residues are missing, the dashed line is in fact shown when the model is shown in cartoon style. In addition, in regular Chimera the dashed line that represents the 4 missing residues remains visible in cartoon style. Thank you for your time. Best wishes, Wout Wout Oosterheert, PhD Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

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Keep color on vseries
by Eric Pettersen 08 Feb '22

08 Feb '22

> > From: "Hunkeler, Moritz" <Moritz_Hunkeler(a)DFCI.HARVARD.EDU <mailto:Moritz_Hunkeler@DFCI.HARVARD.EDU>> > Subject: Keep color on vseries > Date: February 8, 2022 at 8:20:31 AM PST > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Hi, > > I am sure I am missing a simple step here, but I would like to visualize a vseries where each frame is colored according to an underlying model. So, I color all frames with ‘color zone #id near #id distance 15’ and then start the vseries with ‘loop true’ and ‘maxFrameRate 2’. However, as soon as it loops around once, the coloring of all maps is set back to the starting default color. Same thing happens if I just start the vseries twice without ‘loop true’: during the first round, all maps are colored correctly, during the second round all map coloring is reset. This seems to happen only when started from the command line, and not when started from the vseries slider. Is it possible to keep the map coloring when starting the vseries from the command line? I am using the version released 20220204. > > Best, > Moritz

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Re: [chimerax-users] error with open :: 'foreach' has no suffix
by Rangarajan, Amith 08 Feb '22

08 Feb '22

Hi, I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" I am not able to figure out how to debug this. I am using the latest build of chimerax. I will highly appreciate your suggestions on fixing this. best amith

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Extract densities option not available on Segment Map
by Andre LB Ambrosio 08 Feb '22

08 Feb '22

Dear all, probably a silly question: I want to generate a mask o ChimeraX to use later on a local refinement job elsewhere. I managed to segment the cryoEM map and group the regions of interest. However, the "Extract densities" option is unavailable on the "Regions" menu. Likewise, these are unavailable on "Other tools" shortcuts options: Extract, iSeg, ProMod, and ModelZ. Please, what am I missing? I appreciate any help you can provide. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba

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extraction of certain cryo-em density
by Dmitry A. Semchonok 08 Feb '22

08 Feb '22

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Next/previous buttons?
by Oliver Clarke 07 Feb '22

07 Feb '22

Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?

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keeping multi-chain models locked between chains
by Martti Tolvanen 07 Feb '22

07 Feb '22

Dear ChimeraX gurus and demi-gods, I have created a hypothetical multimer model for a protein which has a dimeric structure in PDB (with a large protein-protein interface, considered real), but misses the C-terminal part of the full protein sequence. AlphaFold predicts there to be an amphipathic helix in the missing part, as we also did in our theoretical work. The hypothesis is that the protein could form larger multimers by binding either via the face-face interactions, as in the PDB dimer of catalytic domains, or via helix-helix interactions (tail-tail) as in coiled coils, to create multimers of type AB-BA-AB-BA-AB-BA etc., A being the helical domain and B the catalytic domain. I have created antiparallel coiled-coil-like helix dimers from the helix predicted by AlphaFold with the help of zdock (big thanks for adding the zdock file open functionality in the daily build!) and built a hexamer model using 3fe4 and my best-looking zdock helix pair as templates for orienting the six copies of the monomeric alphafold model. The helix is randomly placed outside of the confident catalytic domain structure in the AlphaFold model, and there is a linker of poor confidence between the domains. With the original orientation of the helix my first-effort hexamer has the catalytic domains partly overlapping, and I'd need to rotate some bonds manually to orient the subunits into realistic positions. I wouldn't care even if I create some serious Ramachandran plot outliers there, when the goal is just to get a visualization for the multimer hypothesis. The problem is that when I rotate any bond in the linker, I either swing one helix out of a coiled-coil pair or one catalytic domain out of the face-to-face dimer interface (depending if I use move small of move large, respectively, in the torsion command). How could I get all six chains into a single chain? I assume that then I would be moving the whole rest of the multimer as a rigid body if I rotate any main-chain bond in the linker regions. ChimeraX session file attached. Cheers, -Martti Tolvanen U of Turku, Finland

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Re: [chimerax-users] chimeraX on wynton ( UCSF-specific)
by Rangarajan, Amith 04 Feb '22

04 Feb '22

Hi, This question is relevant for UCSF only. I have a set of docked poses that i want to analyze using chimera x script ( check ligand RMSDs, distances etc...) . My laptop is not that great, so i can use Wynton, if possible, to do this . is chimerax available on Wynton nodes? if so, please give me a short intro to get started on using chimerax on Wynton. thanks, amith I

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Automate calculation and saving of residues' structural attributes
by André 04 Feb '22

04 Feb '22

Hello! I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline. However, currently the files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of calculating the attributes and exporting their respective files. I searched a lot, and tried some ways to achieve such an automation (using Chimera), but nothing worked. And I also considered using ChimeraX. In particular, I went through ChimeraX Programming Manual ( https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#) but, if I understood correctly, I'd only be able to import chimerax and use its functions in the Python interpreter within ChimeraX (Tools >> General >> Shell). At first, I'd like to import chimerax as a module in a Python interpreter outside of ChimeraX, so that manually opening ChimeraX wouldn't be necessary in order to save the files with the residues' attributes. But, from some other threads in the mailing list, I found that it wouldn't be possible (right?) But I also found out that I could write a .py script which calculates and exports the files with the residues' properties, and then run it with ChimeraX application from the command-line, something like: *chimerax --nogui myscript.py* If that works, I think that my automation problem would be solved! The only problem is that I really couldn't figure out the Python code to calculate and export the aforementioned residues' properties (I took a look in ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/) but I couldn't find what I need, nor more detailed documentation). Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed. I really appreciate any help you can provide! (And thanks to Tom Goddard for suggesting moving the discussion here to the ChimeraX mailing list). Thank you so much, André.

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Is there an output directory command for spin movies or morphs?
by Ralph Loring 03 Feb '22

03 Feb '22

Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Change default palette for sequential coloring?
by Oliver Clarke 03 Feb '22

03 Feb '22

Hi, I really like the option to use custom palettes from colorbrewer etc in ChimeraX for sequential coloring. Would it be possible to allow users to change the palette used as the default for sequential coloring? E.g. I really like "RdYlBu-5 (3-11)", but I can never remember the name or syntax, and for quick jobs I would love to be able to to set the default coloring scheme so it is just set up the way I like it. Cheers Oli

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Coloring Chains Sensitive to Case After Combine
by Anderson, Jacob 03 Feb '22

03 Feb '22

Dear ChimeraX, Really loving the implementation of the combine command in 1.3! After using the combine command to create a model with >30 chains, the resultant model has some chains with the same chain ID but with a lowercase (i.e. #6/D and #6/d are in the model). When I color #6/D (i.e. color #6/D green), this also is coloring chain #6/d. Is this the expected behavior? When I read help:user/commands/atomspec.html it seems that the chain identifier should be case sensitive if both upper and lowercase chain IDs are present. Curious if there is a way to force the case sensitivity.

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"Backbone N-H atoms” as Ball & Stick representation
by Gupta, Arun 02 Feb '22

02 Feb '22

Hello Elaine and team, I am working with Chemical shifts based CS-Rosetta generated NMR structural model of the protein (amino acid sequence 1-84). And, I would like to show the “backbone N-H atoms” in the NMR structural model in a ball & stick representation. The series of command which I have used are as follows Open pdb cartoon suppress false sel #1:1-84 @n,h And finally from ChimeraX GUI interface, I am choosing following set of options Action/Atom style/ Ball & Stick. But nothing happens. It seems I am missing something. Please suggest the way around with this problem. Thanks! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Default Save Location
by William Wang 02 Feb '22

02 Feb '22

Hi ChimeraX Team. Is there anyway to set the default location for the save command as somewhere other than desktop? Thank you William Wang Undergraduate Student Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Building ChimeraX Bundle
by Zeng, Katie 01 Feb '22

01 Feb '22

Dear ChimeraX Users, I'm currently working on a bundle for building lipid membranes and I have a few questions: 1. A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle? 2. Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them. 3. Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them. Thank you so much for your help! Best Regards, Katie

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hbonds and the number of detected interactions
by Enrico Martinez 31 Jan '22

31 Jan '22

Dear ChimeraX users! I have a question regarding calculations of the hydrogen bonds and its visualisation using hbonds. Here is my command: hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color turquoise distSlop 0.4 angleSlop 20 intraRes false So I ignore intraRes (since the ligand is also present in the #1) and calculate hydrogen bonds using default parameters. 1) How can I modify geometric criteria for the calculations (is this distSlop / angleSlop) to increase the distance for the consideration of potential h-bonds ? In particular as you may see on the attached image the bond between the side-chain of the Glu166 and NH of the ligand is absent (I've just checked the same structure using py*ol and it could detect this contact). 2) In the case of another ligand, I could visualize two h-bonds provided by two hydrogens of the side chain of the Gln189 (same residue) with two different oxygens of the ligand. Is this correct? Many thanks for the tips! Yours sincerely Enrico

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ChimeraX 1.4 Download?
by Nayla Abney 27 Jan '22

27 Jan '22

Good evening, Hope you are doing well! I am trying to use your ChimeraX 1.4 download after watching this AlphaFold Protein Complex via ChimeraX Youtube video (https://www.youtube.com/watch?v=6lXeCPuTePs) However, I am having issues finding the download for the 1.4 version because your website only shows the 1.3 download (https://www.rbvi.ucsf.edu/chimerax/download.html) When I try using this version, I am having issues with inputting the sequence in the correct format because I keep getting a sequence argument error. I have tried looking up documentation for this version and this error, however, I am only seeing 1.4 documentation. Could you guide me in the right direction of where I should go ideally for the 1.4 download? I guess my Googling skills could use some help :) Thank you! ------------------------------------------------------ Nayla

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Help viewer is blank after upgrading to Fedora 35
by Nicholas R Silvaggi 26 Jan '22

26 Jan '22

Hello, I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this? Thanks for your help, Nick Silvaggi P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists. Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 372D Phone: 414-229-2647 silvaggi(a)uwm.edu

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Modeller python script
by Mary Liu 26 Jan '22

26 Jan '22

Dear Chimera X team, I'm using Modeller in ChimeraX to build a homology model. Is there a way to look at the python script to know how it works? Thanks Mary

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3Dconnexion
by Wang, Difei (NIH/NCI) [C] 26 Jan '22

26 Jan '22

Hello ChimeraX team, Thanks for developing the ChimeraX! It is easier to use than Chimera. However, I noticed that my 3Dconnexion could not work anymore when I use ChimeraX. Will it be possible to include such a function in the future version of ChimeraX? Thanks, Difei ======================== Difei Wang, Ph.D. Bioinformatician (Contractor) BB/DCEG/NCI/NIH 9609 Shady Grove Rd. Rockville MD 20850 USA Tel: 1-240-276-5092 ========================

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Surface coloring
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the protein-ligand binding visualizations using surface representation for the protein. In this case (please see enclosed example) I used mlp palette moccasin:sienna:sandybrown range -55,55 to make this expression of the protein in the Mountain style :-) Two questions: 1) how can I introduce more "dark" gradients into the cavities (similar to the vulcan) ? 2) is it possible to switch the coloring pattern from such a "realistic" view to the animated "cartoon" style ? 3) Any additional advice for the surface visualisations ? Many thanks in advance! Enrico

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artistic cartoon visualisations
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the improvement of the cartoon visualizations. Here are some options that I have found very cool: preset 'overall look' publication cartoon style coil thickness 0.22 set silhouettes t; set silhouetteColor firebrick; set silhouetteDepthJump 0.02 could you please suggest me something, which may further develop these ideas? In particularly I would like to improve representations of the beta-sheets making the arrow-ends more elongated and cylindrical Many thanks in advance Enrico

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Debian 10 Installation
by Martin Urban 25 Jan '22

25 Jan '22

Dear ChimeraX users, I have a problem with the installation of ChimeraX under Debian 10 buster. I downloaded the ucsf-chimerax_1.3ubuntu18.04_amd64.deb from the official website. I installed it one time with: /sudo dpkg -i //ucsf-chimerax_1.3ubuntu18.04_amd64.deb /and also with /sudo apt-get install .///ucsf-chimerax_1.3ubuntu18.04_amd64.deb./ Both times I get the same error message: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in " " even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. The full error message is as attachment in this mail. I searched the web for an answer and came up with three entries of this mailing list. I followed the described way in these mails, but nothing worked for me (1st mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002797.html; 2nd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002770.html; 3rd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html) Do you have an answer or a solution to my problem? Greetings from Germany -- Martin

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Ribbon Thicken
by Cameron Larson 25 Jan '22

25 Jan '22

Hello, Is there a way to thicken ribbons so I can 3d print a structure? What do you recommend for 3d printing a structure? -Cameron Larson

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