- ChimeraX-users - RBVI Mailing Lists

ChimeraX fetch by PubChem CID
by Elaine Meng 12 Feb '25

12 Feb '25

> On Feb 12, 2025, at 11:41 AM, Alexander Mansueto <alexander.j.mansueto(a)vanderbilt.edu> wrote: > > Can we import pubchem CID molecules to model proteins with lipids? Would be very cool. Hi Alexander, The recommended address for asking ChimeraX questions is the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list CC'd here, see "contact us" on our website or in the ChimeraX menu: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> If PubChem Compound has the coordinates, you can open them in ChimeraX by CID, e.g. command open pubchem:12123 - OR - open 12123 from pubchem ... as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> ...or with menu: File... Fetch by ID, choosing the Pubchem option and specifying the CID in the dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/fetch.html> However, not every entry in PubChem Compound has coordinates available, so I don't know if it will work for your specific molecules of interest. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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steam VR running but still get an error with Vr on command.
by Krishnan Raman 10 Feb '25

10 Feb '25

[cid:5bbc0381-58d6-4058-bc7c-183bcd144645] Steam VR is running and still i get this error. Am i overlooking something? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

there is no amination？？？
by 刘涛 07 Feb '25

07 Feb '25

2 2

Recording MD Trajectory Movie in ChimeraX
by Gourav Das 07 Feb '25

07 Feb '25

Dear ChimeraX users, I have performed MD simulation of a system using AMBER20. The topology and trajectory files are in .parm7 and .nc formats, respectively. I would appreciate your guidance on visualizing and recording the trajectory as a movie in ChimeraX. Thank you for your support. With regards, Gourav Das Research Scholar Department of Chemistry Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Re: Introduction of a proteolytic cleavage in ChimeraX
by Elaine Meng 04 Feb '25

04 Feb '25

> On Feb 4, 2025, at 3:30 AM, Mark Hilge <markhilge(a)icloud.com> wrote: > > Dear Dr. Meng, > [... details removed ...] > Question: In ChimeraX, is there a possibility to introduce a proteolytic cleavage between say Leu112 and R113? This should result in Leu112 with a carboxylate group followed by a TER keyword. > > Many thanks in advance! > Kind regards, > Mark Dear Mark, It depends what you want to use this for. If it's just for a figure, that is totally different than if you were going to do some extensive workflow afterwards. If you have an input PDB file, one "dumb" way is to text-edit it to put the TER card in before opening in ChimeraX. However, that will not add a carboxylate oxygen, there would just be a dangling C=O. If you wanted an OXT you would have to add it "manually," e.g. in the Build Structure tool. However, that will be problematic because it won't want to add the OXT right on top of the N, which is where it would want to go. You'd also have to change the conformation of the chain, e.g. rotate a bond with the mouse mode or the "torsion" command. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> Within ChimeraX, you could use command ~bond to remove bonds. However, if you do this within a chain defined in the input (e.g. PDB SEQRES lines or mmCIF file equivalent), it will then draw a dashed line because it still "knows" they are supposed to be connected within the chain because of the SEQRES records in the PDB file. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> So it's all more complicated than you might think, especially if you wanted everything to be correct for some subsequent modeling workflow. You might instead give the two parts two different chain IDs. One way is to text-edit the PDB file. Another is to open the thing twice, delete the first part of the chain in one copy, delete the other part of the chain in the other copy, and then use "combine" to create a new model that has both parts but with different chain IDs, and then use "save" to save a PDB file of that combined model. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, you would still need to text-edit the PDB file manually so that there are SEQRES records for the two different chains (the two parts of the original single chain) that each contain only the residues for the corresponding part. These are different than the ATOM records that have the coordinates. And I can't even begin to explain how you might do it in mmCIF, all of this is in PDB format only. So if you bothered to do all that, then if you use "addh" it will automatically add the "OXT" because it will finally recognize the new cleaved C-terminus as a real C-terminus. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> For future reference: please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here to ask questions about ChimeraX, omitting any information that needs to remain private. If you send email to me only, it may not get answered. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Suppress errors when using runscript?
by Vorländer,Matthias Kopano 03 Feb '25

03 Feb '25

Hi, I wondered if it is possible to suppress/ignore an error message when executing scripts with runscript. Specifically, I have a script to analyze alphafold (3) predictions and select residue interfaces residues using the interface select command. The selection for each of the five model is then saved in a named selection: # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel This works fine when all models show contacts , however, if one of the models/predictions does not have any residues involved in an interface, the script stops with the error “Nothing is selected by the specifier”. It would be great if the script does not pause at this message. Below the full .cxc script I am using: Best, Matthias # Generate AF contacts for all predictions of an AF3 run # # Usage: # runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name> # The script assumes that five models were generated by AF. It expects the CIF files to be in a sub‐directory # matching the pattern "*model_X*.cif" and the corresponding JSON files in a sub‐directory matching "*data_X*.json" # for each model number X (4, 3, 2, 1, 0). # For the alignment and mseries slider command to work properly, the script assumes no other models are open. echo "Usage: runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name>" ##### Model 4 ##### # Open the structure and its JSON scores for model 4. open $1/*model_4*.cif open $1/*data_4*.json structure last-opened hide show c # Generate AF contacts (using JSON scores) for chain A (or the first chain) alphafold contacts last-opened &/A name model_4_af_contacts_$2 # Create pseudobonds for the contacts and label them with residue names and numbers. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation to a file. save $1/af_contacts_model_4_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_4_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel show interface_residues$2_model_4 style interface_residues$2_model_4 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_4 saveFile $1/interface_residues$2_model_4_buriedArea_300.txt # Color the model for clarity. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_4 and info saved to $1/interface_residues$2_model_4_buriedArea_300.txt" ##### Model 3 ##### # Open the structure and its JSON scores for model 3. open $1/*model_3*.cif open $1/*data_3*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_3_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_3_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_3 sel show interface_residues$2_model_3 style interface_residues$2_model_3 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_3 saveFile $1/interface_residues$2_model_3_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_3 and info saved to $1/interface_residues$2_model_3_buriedArea_300.txt" ##### Model 2 ##### # Open the structure and its JSON scores for model 2. open $1/*model_2*.cif open $1/*data_2*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_2_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_2_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_2 sel show interface_residues$2_model_2 style interface_residues$2_model_2 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_2 saveFile $1/interface_residues$2_model_2_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_2 and info saved to $1/interface_residues$2_model_2_buriedArea_300.txt" ##### Model 1 ##### # Open the structure and its JSON scores for model 1. open $1/*model_1*.cif open $1/*data_1*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_1 sel show interface_residues$2_model_1 style interface_residues$2_model_1 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_1 saveFile $1/interface_residues$2_model_1_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_1 and info saved to $1/interface_residues$2_model_1_buriedArea_300.txt" ##### Model 0 ##### # Open the structure and its JSON scores for model 0. open $1/*model_0*.cif open $1/*data_0*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_0_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_0_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_0 sel show interface_residues$2_model_0 style interface_residues$2_model_0 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_0 saveFile $1/interface_residues$2_model_0_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_0 and info saved to $1/interface_residues$2_model_0_buriedArea_300.txt" ##### Final Steps ##### # Move all models (except the last-opened) to a common group (optional) mm #*&~last-opened&/A to last-opened&/A # Create an mseries slider for the five models. mseries slider #1-5 title $2 name $2_slider mseries #1-5 echo "Use the slider to go through the models!" echo "Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 300 Angstrom or more) have been saved in the input folder for each prediction" echo "You might want to increase stringency by calcualting the overlap between all predictions"

2 1

Getting two color keys in the same ChimeraX session
by Elaine Meng 03 Feb '25

03 Feb '25

> Begin forwarded message: > > From: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Re: key command > Date: February 3, 2025 at 11:52:12 AM PST > To: Fabian Glaser <fglaser(a)technion.ac.il> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Reply-To: chimera-users(a)cgl.ucsf.edu, Eric Pettersen <pett(a)cgl.ucsf.edu> > > Hi Fabian, > There is no direct support for multiple keys, but it is pretty easy to “trick” ChimeraX into showing multiple keys. You would create your first key normally, getting it exactly the way you want it to look before creating the next key. You create the next key with the following Python code: > > from chimerax.color_key.model import ColorKeyModel > m = ColorKeyModel(session) > > If the above was in a file ending in ‘.py’, you could just use the ‘open’ command to run it and create the key. I’ve attached a file with that code in it for convenience. Once you have created the key, then all operations that affects keys (like the ‘key’ command) will affect the new key and leave the original key as is. If you had the Color Key tool up, it will continue to show the old values. Just close it and re-open it to show the new values. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Feb 3, 2025, at 6:31 AM, Fabian Glaser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> We would be interested to add more than one key color bar in the same chimerax session. But we noticed the key command allows only one color key can be present at a time. >> >> Is there a way to add more than one color key in the same session? >> >> Thanks a lot, >> >> Fabian >> >> >> Fabian Glaser, PhD >> >> Technion Centre for Structural Biology (TCSB), Computational Section, Head >> Technion Human Health Initiative (THHI) >> Technion - Israel Institute of Technology, Haifa, Israel >> fglaser(a)technion.ac.il >> +972 (0)48293701 >> >> >> >> _______________________________________________ >> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Grid mode and multiple viewports
by Roden Deng Luo 03 Feb '25

03 Feb '25

Hi, I find there is a `tile` command. After I enter the tile mode, the zoom is global. I guess `tile` is implemented by transforming the active models in the global scene explicitly. I wonder if there is a way to have the zoom independent for each model, similar to the grid mode in PyMol. A further question, more from a developer's perspective, is whether having multiple 3D rendering viewports in ChimeraX is possible. I imagine each viewport can have its own active models in the scene and its own camera. Different cameras and other operations might be synced upon users' request. This video (https://youtu.be/7KZ1P-nPav8?si=Z1hiBBuRiWop2WFC) demos the feature (in an old version of Houdini). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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aligning maps generated by chimeraX
by msteves＠berkeley.edu 31 Jan '25

31 Jan '25

Hello, I'm new to Chimera, but would like to use it to generate surface maps of electrostatic potential and hydrophobicity, then output for further analysis. I've generated maps using coulombic and mlp commands, and successfully saved these to .MRC format. However, when I go and read these files, the dimensions of the maps are different, so I'm not sure how to properly overlay these maps in my later analysis. Is there a way to have Chimera generate maps only within a given spatial range, so I end up with maps of the same size? Or another way you would recommend going about this? In later analysis I'd also like to make use of the SAS calculated by Chimera, and I imagine I will also have difficulties properly aligning the surface to the maps, so any advice on this would also be greatly appreciated! Thanks, Megan Steves

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Question about Surface Volume Overlap Calculation
by John Watters 31 Jan '25

31 Jan '25

Hello, I was wondering if anyone had any tips/tricks/useful functions for quantifying the volume of the overlap between two surfaces in ChimeraX? I am looking specifically to make a metric to compare steric clashes of molecules in different orientations. Thank you for any help you can provide! Best, John

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Add help for reusable ChimeraX script that takes command line arguments?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi, It’s me again 😉 I wondered how I can add a help page to a re-usable ChimeraX script that is run via runscript. I saved the following script in my ChimeraX presets: #Required arguments: first is the uniprot ID, second is the model ID that will be used for mapping! alphafold fetch $1 #get the missense data open $1 fromDatabase alpha_missense format amiss #associate missense data to structure mutationscores structure $2 #label each residue with matric mutationscores label #1 amiss height 3 #define a new score called avg by avergaing over all substitution scores mutationscores define avg fromScore amiss setAttribute true combine mean #color by avg missense score color byattribute r:avg $2 target csab palette palette bluered range full #scale cartoon by acg missense score cartoon byattribute r:avg #!$2 and then defined an alias in my startup commands so I don’t need to type the full path alias map_missense runscript /Users/matthias.vorlaender/Documents/ChimeraX_presets/map_missense.cxc $1 $2 Is there a way to display the expected user inputs when the script is called without arguments? Cheers, Matthias

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Feasibility of selecting chain ID via uniprot ID?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi again : ) When comparing structures from different sources (such as different PDB depositions, or an Alphafold structure), it is always tedious to figure out which chain belongs to which protein (especially for large structures like spliceosomes) for consistent coloring or alignment. I wondered if it would be technically feasible to use the uniport ID to match a specific chain directly, since the association between chain ID and uniport ID should be present at least in structures from curated databases such as the PDB and Alphafold. So the ambition would be to be able to use ‘color IF4A3_HUMAN red’ directly, without having to look chain IDs. An added bonus would be to be able to skip the species identifier, in case you have models containing IF4A3_MOUSE and IF4A3_HUMAN, and match both with IF4A3 …. Would be curious to hear your thoughts. Thanks a lot, and best wishes, Matthias

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Encode: saving a movie on a Windows laptop, and colouring residues in the multiple sequence
by Anne-Frances Miller 30 Jan '25

30 Jan '25

Dear ChimeraX My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please? Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV. Thank you, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/ Visiting Fellow, Einstein Foundation of Berlin

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Possible to plot attribute value over sequence?
by Vorländer,Matthias Kopano 29 Jan '25

29 Jan '25

Dear ChimeraX team, I wondered if it is possible to generate a line or scatter plot of an attribute value (B factor, Alphafold pLDDT scores, or AlphafoldMissense score…) over the residue number? For example something like this (taken from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089116) : [cid:image001.png@01DB7242.B1C3F8A0] Specifically, for the AlphafoldMissense data, such a plot would be more informative then the default histogram that is displayed when fetching the scores when looking for functional hotspots in your POI. Many thanks, MAtthias

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Chai discovery data
by Reza Salavati, Prof. 29 Jan '25

29 Jan '25

Hello, I have downloaded the Chai discovery data in .npy and .json file formats. How can I open these files in Chimera X? Thank you Reza

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ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Francisco Murphy Pérez 29 Jan '25

29 Jan '25

``` root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: Unsatisfied dependencies: ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). libgdk-pixbuf-2.0-0 set to manually installed. Summary: Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 ``` From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash?

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Re: [Chimera-users] How to subgroup the chains of oligomer pdb
by Elaine Meng 28 Jan '25

28 Jan '25

Hello, If you are asking about ChimeraX, it is better to use the address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, instead of the older Chimera address. I don't know if this is exactly what you want but you can give a name to any set of atoms. For example, open your-oligomer.pdb name frozen mygroup1 #1/A-F name frozen mygroup2 #1/G-L select mygroup1 color mygroup2 orange See ChimeraX "name" command (your name can be something else, like gp20 instead of mygroup1): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Or, a totally different thing you could do is split the model into two different models, for example, open your-oligomer.pdb split atoms #1/A-F atoms #1/G-L That would make your model #1 into two separate models #1.1 and #1.2 with the specified sets of atoms. See ChimeraX "split" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> You can also change names of models (what is shown in the Models list) using the "rename" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 24, 2025, at 8:14 PM, sktewary via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Friends > > I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F. > > Please give your feedback if chimerax can do it, how to do it?

2 1

Limit blast search to species
by Vorländer,Matthias Kopano 28 Jan '25

28 Jan '25

Dear ChimeraX team, I wondered if it is possible to limit a BLAST search to only a single species when querying a selected database. This would facilitate identifying homologs in your favorite model organism, rather than picking up the most closely related homolog overall (i.e when using the alphafold database). Many thanks, Matthias

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Clustal alignment
by Rosaleen Calvert 28 Jan '25

28 Jan '25

Hi. Apparently alignment is newly available in Chimerax 1.9. I cannot find how to do this in Tools: sequence or Tools: structure analysis. From Rosy Calvert

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movie crossfade
by Enrico Martinez 27 Jan '25

27 Jan '25

Dear ChimeraX users! I am recording a short animation demonstrating my docking ensemble # start recording movie record ## play DOCKING movie from end to begining coordset #1 96,1,-1 wait 96 Would it be possible to add a smooth transition between each frame (docking pose) using the movie crossfade command ? If so, how should this command be placed in the script ? Many thanks in advance ! Enrico

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Fwd: ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Eric Pettersen 27 Jan '25

27 Jan '25

Greg, I’m guessing this is yours… —Eric > Begin forwarded message: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Fwd: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) > Date: January 23, 2025 at 3:45:29 PM PST > To: chimerax-programmers(a)cgl.ucsf.edu > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > > Anybody? > >> Begin forwarded message: >> >> From: Francisco Murphy Pérez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) >> Date: January 19, 2025 at 1:22:00 PM PST >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >> Reply-To: Francisco Murphy Pérez <francisco.murphy(a)ibt.unam.mx> >> >> ``` >> root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb >> Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' >> Some packages could not be installed. This may mean that you have >> requested an impossible situation or if you are using the unstable >> distribution that some required packages have not yet been created >> or been moved out of Incoming. >> The following information may help to resolve the situation: >> >> Unsatisfied dependencies: >> ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable >> >> root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb >> Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' >> libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). >> libgdk-pixbuf-2.0-0 set to manually installed. >> Summary: >> Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 >> ``` >> >> From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash? >> >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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ChimeraX question - Diana Mayorga
by Diana Carolina Mayorga Gonzalez 27 Jan '25

27 Jan '25

Hi, Hope you are well. I would like to know if I can do these transparent bubbles in ChimeraX showing the atoms stick as well. If it is possible, could you help me with a small tutorial, please? [cid:add7b0b3-f091-48a9-bc44-329473b06f2e] Thank you so much in advance, Diana Carolina Mayorga G PhD Student Yannick Doyon Lab Research Center - Université Laval Department of Reproduction, mother and youth health (RSME) Québec, Canada

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Re: movie with model label/name
by Elaine Meng 26 Jan '25

26 Jan '25

Dear Saif, To ask questions in the future, we recommand that you please use the mailing list for the appropriate program (chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> for Chimera, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> for ChimeraX). If you mail me individually your question may not get answered. I will answer for ChimeraX since that is our preferred program now -- Chimera is no longer developed. In general, this topic is covered in the ChimeraX "making movies" page: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> You can do all of this with a command script using several commands. There is a "morph" (atomic) or "morph maps" (density maps) command to do the morphing. You would probably change the display (colors, styles, etc.) to how you want it for your movie and then save a session. Then, to work on making a movie you would create a command script that applies to the session. The reason to save a session is so you can avoid redoing the same setup calculations, coloring, etc. every time you run the script. You can do all that stuff first and then save a session. Usually working on the script takes several days, so you would just restore your session and then continue working on the script. The script would contain what you actually want to show in the movie. You can play back an atomic morph with "coordset" and show/hide labels with "2dlabel" and you can do all kinds of other stuff as well, like zoom and rotate. You may also want to save positions in your session file (see "view" command) and then during the movie script, restore those different positions. When the movie script contains what you want to show in your movie, which is usually a long interative process after you play it back several times and keep changing the commands, then you would add the movie-recording commands (see "movie" command) to start recording at the beginning and save the movie file at the end. There are examples in our "making movies" page and links therein to the help for the commands mentioned above as well as movie-making tutorials. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 26, 2025, at 5:53 AM, Md Saiful Islam - MRC LMB <sislam(a)mrc-lmb.cam.ac.uk> wrote: > > Dear Elaine > Just wondering, is there any script to make movies to show the conformational changes between multiple models with the labeling of each of the models shown. > For example, I want to make a movie to show a morph between three cryoEM models where I want to label the three models while morphing from model 1 to model 2 and from model 2 to model 3. > > Accept my apologies if you already shared this before. > > Many thanks for your help. > > Kind Regards > Saif

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Confirming coordinate axis
by Abhinaba Das 24 Jan '25

24 Jan '25

Dear ChimeraX-users, I'm writing to ask if there is a way to view the x,y,and z axis live while model building. I've a helical map generated in CryoSPARC which has a D1 symmetry. I could generate the asymmetric unit (ASU) for the corresponding C1 reconstruction but having issues applying D1 symmetry. The approach I've taken is to make a diheral copy of the C1 ASU (turn y 180 center <mapId> coordinateSystem <mapId> model <modelid>; followed by combine command). This should generate the dihedral ASU, and if the helical symmetry is applied should generate the symmetric copies (?). But seems not to be working.. I've assumed that the dyad axis is along the y-axis (cryosparc says for its output map). Just wondering if the axes are aligned.. Thanks, Abhi

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openmmforcefields
by Lewandowski, Jozef 24 Jan '25

24 Jan '25

Hi, I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX? Thanks, Józef

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Surface Color
by Hansen, Bryan (NIH/NIAID) [E] 24 Jan '25

24 Jan '25

Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Assigning a custom net charge for a ligand using dockprep
by Jade Shi 24 Jan '25

24 Jan '25

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly? Thanks a lot! Jade

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Draw and build secondary structures interactively
by Roden Deng Luo 22 Jan '25

22 Jan '25

Hi, I know there is a tool and command "build". But it is not that interactive. I wonder if there is a feature in ChimeraX (or any other tools) that can allow the user to draw in 3D space (or 2D) lines and then specify some segments as alpha-helices and some other segments as beta-sheets. I imagine the generated structure can be a backbone populated with G (glycine). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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"forEach" command to open multiple pdb from multiple directories and save images there ?
by Vincent CHAPTAL 21 Jan '25

21 Jan '25

Hi, I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. I'm using the forEach command to open all the results and run the script to create an image, and it works very well: open script.cxc forEach /PATH*/ranked_*.pdb script.cxc: open reference-structure.pdb match #1 to #2 color #*/B green color #*/C red color #*/D blue view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41 I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location: save /PATH*/$file.png doesn't work because the /PATH*/ is not recognized as an existing directory. save /$PATH*/$file.png gives the same error. If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. Could you let me know how to save in the folder where the .pdb was read from? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

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Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

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No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

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Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

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Question about the tool Find Cavities
by svle＠tiscali.it 16 Jan '25

16 Jan '25

Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio

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pb with alphafold error plot when we used dimer
by Jean-François Bureau 15 Jan '25

15 Jan '25

Hi, When I stimulate dimer using alphafold3, it is not possible to load the error plot since Chimerax is waiting to have the data of the first protein and find that of both. Best JF Bureau

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Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
by Elaine Meng 13 Jan '25

13 Jan '25

Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2(a)gmail.com> wrote: > > Oh shoot! > You are right, > > I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html > I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced. > > Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow. > > This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf > > THANK YOU for answering on a Sunday!! > Anne-Frances > >

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abbreviation for transparentbackground please
by Anne-Frances Miller 12 Jan '25

12 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Problem upgrading to the latest version 1.9
by svle＠tiscali.it 09 Jan '25

09 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

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Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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Assistance/guidance with ChimeraX
by Mahesh Chandrasekharan 03 Jan '25

03 Jan '25

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package! It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX? 2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer? Thank you, Best, Mahesh Mahesh B. Chandrasekharan, PhD Assistant Professor of Radiation Oncology Investigator, Huntsman Cancer Institute Adjunct Assistant Professor of Hematology & Hematological Malignancies University of Utah School of Medicine 2000 Circle of Hope Room 3715 Huntsman Cancer Institute Salt Lake City, UT 84112-5540 Phone: 801-213-4220 Administrative Assistant: Coreen Rankin (801-585-3599) Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

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Getting average of PAE values for a given region / interaction
by David S. Fay 02 Jan '25

02 Jan '25

Greetings and Happy New Year to All! My question is about broadly protein-protein interactions (PPIs. Last year several manuscripts came out proposing new metrics for assessing PPIs. This was in logical response to the growing understanding that ipTM (alone) is a fairly flawed metric, particularly for detecting interactions that involve a small number/fraction of the total residues. For those interested, I’ve pasted links to three such papers below (Coincidentally one is from a former roommate's lab, which I didn’t notice until recently!). Some may be easier to use than others (have GUIs). Tom Goddard and I emailed back and forth a bit about the relative merits of some of these metrics - nothing is perfect obviously (thank you again Tom). With respect to ChimeraX, I was wondering if there was a way to extract average PAE values after employing a cutoff. For example, "alphafold contacts /A distance 5 maxPae 5” will tell me that are "54 residue or atom pairs within distance 5 with pae <= 5”. But what if I want to know the average of those 54? Along those lines, for some PPIs there may be several spatially separated interfaces, with each one contributing to the total number. Is there an easy way to obtain the average and other metrics for each one? Some of this information I could probably find in my clunky (borderline boomer) way, by filtering, adding, and averaging values from the pairwise data (perhaps made easier by Predictome). Lastly, drawing rectangles on the PAE plot does a great job of giving coordinates and the average PAE, but it doesn’t give the range or other potentially useful data, such as the number of PAE<5 values etc. I guess I’m thinking that it could be very useful to be able to get metrics for a prescribed region of the PAE plot simply by drawing the rectangle. (And maybe there is but I missed it.) Those are my questions and thoughts. But I also wanted to express my gratitude for the ChimeraX software, and even more, the people working at ChimeraX who are always exceptionally responsive and helpful. David https://www.biorxiv.org/content/10.1101/2024.02.19.580970v1 https://www.biorxiv.org/content/10.1101/2024.10.23.619601v1 https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1 David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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get help with changing the cartoons ribbon to ball sticks
by Nhi Hoang 02 Jan '25

02 Jan '25

Hi. I am a sophomore at Le Quy Don High School in Danang City, Vietnam. I am using ChimeraX to display a model for my little project, and I have found a small trigger that I want to get help with. My problem is I cannot change the cartoon of selected residues from ribbons to ball sticks, after I have preset the model with cartoon ribbons. I wonder if this problem is due to the application and its limits or because of my device. I have attached an image presenting the coding and the model for a clear description of my problem. If possible, I am really willing to receive some advice from you in tackling this problem. Thank you very much. Best, Nhi Hoang. [image: image.png]

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Vector in ChimeraX
by Vitali James 30 Dec '24

30 Dec '24

Dear ChimeraX, Can you please help me to connect two pseudo-atoms by vector in ChimeraX. In the attached image (chimera.png), it was smoothly done in the past, but now the same file looks like a dotted line in chimeraX( e.g vector.PNG). Is it possible to control the color and style of this dotted vector line? best regards J. Vitali

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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Unable to show interactions between bases and protein
by ADINDA 27 Dec '24

27 Dec '24

Dear Chimerax team, Hi, I am trying to find the interactions between my RNA and protein but have been unable to do so. I've been using the "contacts" function but it's not been working as expected. The command line that I gave was: contacts #1.2 restrict #1.1 makePseudobonds true reveal true log true where #1.2 is my RNA and #1.1 is my protein. Even when I switch the positions of #1.2 and #1.1, it still doesn't work (0 contacts shown). Do you have any tips on how I can rectify this? Happy holidays! Best regards, Adinda

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How probe radius should affect exposed surface area?
by Alon BenDavid 25 Dec '24

25 Dec '24

Hi, I am trying to measure the exposed surface area of lysine residues in DNaseI (4AWN). I am using the "measure sasa" command. To my surprise, when I am increasing the probe radius (1.4 A, 5 A, 10 A etc.) I receive larger exposed surface area. Is that OK? Many thanks, Alon

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cartoon style setting
by junjie han 23 Dec '24

23 Dec '24

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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"straightening" or stretching disordered residues from alphafold models
by Daniel Elnatan 19 Dec '24

19 Dec '24

Hi folks, I’ve been playing around with AlphaFold to get protein structures and visualizing them in ChimeraX. For some proteins with a lots of disordered regions (e.g. between non-interacting, well-folded domains), the ‘noodles’ end up being a visual clutter. So I wrote a custom python function to be used in ChimeraX that would ‘straighten’ or stretch selected residues (typically the disordered or low pLDDT regions) by simply assigning torsion angles for a more ‘straight’ structure. I do this via the `Residue.set_phi()` and `Residue.set_psi()` methods. Here’s a link to my Python script: https://github.com/delnatan/colabfold_chunker_utils/blob/65f2419425de300df5… The command is run simply with `straighten #1:13-20`. Now when there are multiple chains within the same model, altering the torsion angles may actually move the relative positioning between the chains. Is there an easy way to avoid this? perhaps by passing an extra argument as ‘reference’ so one can place the structure back to its original coordinate for the reference residues. I’m not too familiar with the programming API just yet, but what is the correct way to do this? Maybe that the reference coordinates can be saved before assigning the torsion angles, and a transformation matrix can be computed only for the reference region between the original and moved structure. The altered chain can then be moved back by applying this transformation matrix? Thanks! -Daniel

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