- ChimeraX-users - RBVI Mailing Lists

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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Model grouping and next/previous buttons
by Oliver Clarke 02 Jul '25

02 Jul '25

Hi, I use the next/previous buttons (sequential display controls) in the model panel quite a lot for quickly flicking between 3D classes - they are very handy for this! I would like to be able to use the same buttons for switching between model/map pairs, but there is no way to do this currently. I expected that if I grouped models by using the rename command to make (for example) the map a sub-model (e.g. model #1, map #1.1), then the next/prev buttons would switch between the model groupings, but this is not the case - it still treats the sub-models as independent models. Would it be possible to revisit this logic so that if a "base-level" model like #1 is selected, next/prev will switch between model groupings, while if a member of an ensemble is selected (say #1.1), it will cycle through members of the ensemble? Also, would it be possible at some point to add a GUI option for grouping models - perhaps a button in the model panel that allows for automatic grouping of the selected models? Cheers Oli

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Check waters with a full density map?
by Murpholino Peligro 01 Jul '25

01 Jul '25

Dear all I got a pdb and a mtz file (from phenix.maps) with: Number of columns: 11 label #valid %valid min max type H 23487 100.00% 0.00 56.00 H: index h,k,l K 23487 100.00% 0.00 39.00 H: index h,k,l L 23487 100.00% 0.00 26.00 H: index h,k,l 2FOFCWT 23337 99.36% 0.01 1113.30 F: amplitude PH2FOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees 2FOFCWT_fill 23487 100.00% 0.01 1113.30 F: amplitude PH2FOFCWT_fill 23487 100.00% -180.00 180.00 P: phase angle in degrees FOFCWT 23337 99.36% 0.00 836.89 F: amplitude PHFOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees ANOM 19860 84.56% 0.00 149.58 F: amplitude PHANOM 19860 84.56% -179.97 179.99 P: phase angle in degrees (as reported by phenix.mtz.dump) I open both in chimerax with open /home/murph/doc/pdbs/mol1/mol1.pdb open /home/murph/doc/pdbs/mol1/mol1_map_coeffs.mtz structureModel #1 (clipper already installed) If I do tools->structure analysis->check waters and choose the model (now id #1.2) and the 2fofc map (#1.1.1.2) I got a warning saying "Some (or all) atoms lie outside the volume, continue anyway?" If I continue anyway... some waters with density do have a 0 in the density column... This is, I think, because by default the density is not displayed around all atoms of the model (huge models would crash the computer, right?).. so maybe I just need to show the density around all the atoms in the model... How do I do that? (I thought that 'volume unzone' was the magic command but that only shows a bigger cube of density around the center of rotation, instead of the smaller sphere of density). Thanks

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BIOMT output
by Sui, Haixin (HEALTH) 01 Jul '25

01 Jul '25

Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What's This<https://oer.ny.gov/system/files/documents/2023/11/personal-pronouns.pdf>?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui(a)health.ny.gov<mailto:haixin.sui@health.ny.gov> www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory<http://www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory>

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