August 2026 - ChimeraX-users - RBVI Mailing Lists

Using Blotz in ChimeraX 1.12 issue
by Ferguson, Connor 19 Aug '26

19 Aug '26

Hello, I am attempting to examine the interaction of a viral RdRp with single stranded RNA. I downloaded Blotz as prompted, but it ran into an error downloading. I deleted the folder and redownloaded it with seemingly no issue. However, When I put in the RNA alone in an attempt to also get the secondary structure of the ssRNA, or when I put both the RNA and the predicted protein structure, I get the error message "Your Boltz installation does not have a molecular structure for PDB chemical component dictionary code ALA either because that code is new or is mistyped. You can try specifying that ligand using a SMILES string from https://www.rcsb.org/ligand/ALA instead of using its CCD code." I do not know why this message is occurring because even with the RNA alone this occurs (which the RNA should not care about alanine?). Any assistance or guidance on this matter would be greatly appreciated. Connor Ferguson Graduate Student, Virology Lab Teaching Assistant Department of Biological Sciences The University of Tulsa 800 South Tucker Drive Tulsa, OK 74104

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Change default molecule display to cartoon only (hide atoms)
by ramy.kazan＠ibpc.fr 18 Aug '26

18 Aug '26

Hi all, When I open a large model (e.g., a ribosome) in ChimeraX, the default display style shows it as atoms in the spheres style. I’d like to change this so that, by default, all atoms are hidden, and the model is displayed as a cartoon only. I’ve created an alias with the necessary commands and mapped it to a function key for quick adjustments. However, this approach has a limitation: after customizing one model (e.g., showing specific residues as atoms), opening a new model and using the function key overwrites the customized residues, applying the "cartoon-only" style to all open models. There must be a setting to adjust this behavior, but I haven’t been able to find it. I also recall reading that ChimeraX treats small and large models differently—perhaps based on the number of chains or residues—but I can’t remember the exact rules. Could someone point me to the correct way to set this as the default behavior for all new molecules? Thanks for your help! Best regards, Ramy

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PAE and ipTM scores
by Timothy Springer 18 Aug '26

18 Aug '26

The PAE viewer in Chimerax is wonderful. I can delete residues with low confidence pLLDT in the AF3 model (B factor <55) and the PAE viewer still works (only problem is deleting whole chains). Is there a way to delete the same residues and get revised pLLDT scores? I want them per interface in a multichain complex. - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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Regarding playing a series of volumes that are not a series
by Nour Mustafa 11 Aug '26

11 Aug '26

Dear All, I was wondering if there is a way to play a few volumes as a series when they are not in fact a series? I tried running 'vseries play' then listing the volumes individually, e.g. (vseries play #1,2,3) I tried grouping them and running vseries play again with the group's ID, but that also didn't work. Or is there a way to 'label' a group as a vseries so I can run that command, for example? I couldn't find a solution through my search. The volumes were initially a group, but I had to flip them on the z-axis and that broke the series and resulted in separate individual volumes. Sometimes I also want to compare volumes that are not a series by playing them. Thank you all in advance. Kind regards,

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clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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Feature request: expanded CORS options for remotecontrol
by Rich Waldo 07 Aug '26

07 Aug '26

Hello! Thank you for the work you do making structural biology possible! I was wondering if it would be possible to allow the remotecontrol rest start cors parameter to accept a list of allowed origins in addition to true (which I imagine would become an alias for http?://localhost:*,http?://127.0.0.1:*) or false. I have a browser extension I've written to make downloading volumes from CryoSPARC easier and I'd like to tell ChimeraX to first try opening the destination filename and only download the volume if that fails, but since my origin is not localhost I'm blocked by CORS and can't tell whether opening the volume succeeds or fails.

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Opening a PYMOL pse file
by James Prestegard 07 Aug '26

07 Aug '26

Is there a simple way to open a PYMOL pse file in chimera?

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cartoon style setting
by junjie han 07 Aug '26

07 Aug '26

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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sequence viewer colors following a select
by Steven Brawer 07 Aug '26

07 Aug '26

A basic question. Example with one model. When I make a partial selection by click-drag in a sequence viewer , which turns the sequence bright green (in the sequence viewer), then ctl-click in the background of the graphics window to deselect, that bright green color in the viewer turns brown, as below. What does this mean? Why does it do this? How to restore the original coloring? When I run the command sequence chain /A, it apparently creates a new instance of the sequence viewer (deleting the old instance). This is OK with just one model. The problem with this is that if I have several models and do this, it puts the new instance at the bottom of the other sequence viewer instances, so I have to move it if I want the same physical order as in the Model pane. This becomes annoying fast. Is there a way to restore the original coloring in the sequence viewer without completely replacing the original instance of the sequence viewer with an new instance, and leaving it where it is (in the case of several models). Thank you Steve PS: I have ransacked the documentation and tried Google, but have not found an answer. This does not mean the answer is not there, only that I missed it or didn't understand it when I saw it.

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Feature Request
by Nour Mustafa 04 Aug '26

04 Aug '26

Dear All, I was wondering if it would be possible to add a feature to the 'Erase' tool that allows us to change the shape from a sphere. It would be nice if I could just 'push in' or 'pull out' at the sphere to make it into any irregular shape I want. It would make creating masks, etc. very convenient. Sorry if this is already available, I haven't been able to find something similar from my search. Kind regards,

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