- ChimeraX-users - RBVI Mailing Lists

How to get just model name
by Alexandra Zahradnikova 09 Jul '25

09 Jul '25

Dear All I would like to extract just the model name (as a variable) from a model, to write into an output file with other data. However I am not able to find in the help how to do it - I can output all model information ("Model info") to the log but not to see just model name. Is that possible? Thanks in advance Best regards Sasha

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XYZ basis vectors
by Jan Hofmann 09 Jul '25

09 Jul '25

Hello, how can I show the XYZ basis vectors somewhere next to my structure in ChimeraX? I found the .bild datei but I don't want the arrows in my structure, rather outside, next to it, like in Crystalmaker. It would be really helpful to have the basis vectors to compare orientations with other images. Thanks a lot. Best, *Jan Hofmann, M.Sc.* *PhD Candidate, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 577, Chemistry

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Changing bond color in Chimerax
by khaja faisal tarique 08 Jul '25

08 Jul '25

Hi I am trying to color different bonds with different colors in ChimeraX, but when I select one bond and change its color so it gets applied to all bonds. Is there any trick to do that ? What I am doing is the Cltr+Bond to select a bond then changing color to that selected bond. But I do not why the change is applied to all other bonds. Any help would be appreciated Faisal --

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Coloring an Isosurface Using a Second Cube File in ChimeraX
by mohyeddine.taleb 08 Jul '25

08 Jul '25

Hi, I would like to ask how to color a given isosurface (built with the commands open cube1.cube and volume #1 level 0.02 style surface) using the values from a second property stored in another cube file, cube2.cube. Please note that the two cube files describe exactly the same grid. I have also attached an example showing the interaction between two water molecules. Best regards, Mohyeddine Taleb

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Request to help in command panel in chimera X 1.10
by Singh, Prashant Kumar 08 Jul '25

08 Jul '25

Hi, I have recently downloaded Chimera x 1.10, in which I am trying to change the size of sticks and spheres in ball and stick model but the commands I am trying to were not working with error message "Expected a keyword" Here are the commands which I am using Style stick/sphere set stick/sphereRadius 0.3 setattr Radius 0.3 target #3 set stickRadius 0.3 target all size #1 ballScale 1.5 size #1 ballScale 1.5 size #1 ballScale 1.5 setattr m ballScale 0.5 style ligand ball vdw scale 0.8 set stickRadius #3 0.35 set stickRadius 0.3 target sel set stickRadius 0.3 target all set stickRadius 0.3 target all set stickRadius 0.3 target all Unfortunately none of them is working in my command line, will you guys plz help me to to change the size of sticks and sphere in ball & stick model. i am using iMac computer. Best regards Prashant

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Displaying atomic serial numbers
by Michael Patzschke 08 Jul '25

08 Jul '25

Hello, I have a seemingly trivial problem. I have a small molecule and I want to display the serial number of all atoms. Under “Action->Labels->Atoms->Name” I can get atom names, but these are not what I want. I want the atoms numbered as they appear in the .xyz file. Is this possible? Kind regards, Michael

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Unsescribe
by Felipe Munoz Gonzalez 04 Jul '25

04 Jul '25

Hello, I want to unsubscribe of this list thanks

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Boltz-1 data privacy
by Dario Passos 03 Jul '25

03 Jul '25

Dear ChimeraX team, I have a question regarding data privacy when using the Boltz-1 structure prediction tool within ChimeraX. Is the input or output data temporarily or permanently stored, logged, or shared in any way by UCSF, ColabFold, or any third-party services? Is there an option to ensure that all data remains strictly local and is not stored externally? Thank you, Dario

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Coot-like navigation?
by Murpholino Peligro 02 Jul '25

02 Jul '25

Can we navigate the protein model like in coot? spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1 Can you point me in the right direction? Do I have to use aliases or is it something more complicated? Thanks

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rainbow separate color for each residue
by Rebecca Grace 02 Jul '25

02 Jul '25

Hello ChimeraX, Greetings! I've never asked a question, but I need to expedite solving this issue, so thought the time is now. :-) (I should also add, thank you for Chimera and then Chimera X, it has been so beneficial to my research and presentations!) Several months ago I used rainbow to color a range of residues on my structure. Now I am trying to recreate it on a different model and I can't seem to recapture the detail where every residue is delineated versus a continuous gradation across the selected region. I've searched and read several help emails etc, and maybe if I was a more expert user I would understand this from the usage/help entries about rainbow, but alas, I cannot recreate it. Please let me know how I did this?? Thanks for any help! Cheers, Bec Here is the past way that I want to recreate: *notice how each residue of tube helix has a separate color whereas the next image has no separations [image: image.png] And here is the way I can only seem to get the program to do today: [image: image.png]

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