- ChimeraX-users - RBVI Mailing Lists

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 --

2 5

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.

5 5

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

2 1

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/

1 0

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.

4 8

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

2 1

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

3 4

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

2 3

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

3 3

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

3 4

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

3 5

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

4 4

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?

2 1

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

3 7

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

2 1

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

3 13

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/ >

1 0

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

2 1

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

1 0

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

3 2

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

3 2