- ChimeraX-users - RBVI Mailing Lists

How to define axes in chimeraX
by Zhao, Bingchun (NIH/VRC) [F] 10 Feb '22

10 Feb '22

Hi, I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools • Structure analysis • Axes/Planes/Centroids • Define axes But I wasn’t able to find out the equivalent function in chimeraX. Would you please direct me to that function in ChimeraX? Thank you so much! Best regards, Bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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Show atom style as spheres and stick simultaneously
by Mary Liu 10 Feb '22

10 Feb '22

Dear Chimera X users, Is it possible to show atom style as spheres and stick simultaneously with spheres displayed as dots or mesh so the stick is still visible within sphere dots? Thank you Mary

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Loading AlphaFold output
by Daniel Trejo Banos 10 Feb '22

10 Feb '22

Hello everyone, I have the results from some AlphaFold runs, is there a way to open them with ChimeraX, so I can see the plDDT, without needing to run Alphafold from within ChimeraX? Thank you and best regards

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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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