January 2025 - ChimeraX-users - RBVI Mailing Lists

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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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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