- ChimeraX-users - RBVI Mailing Lists

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?

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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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