- Chimera-users - RBVI Mailing Lists

help
by Claire Ellena 15 Apr '26

15 Apr '26

Hello, can you help me. I don’t know where the error is

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Unable to make a distance for a particular residue
by SHUBHRAJYOTI PANDA 06 Apr '26

06 Apr '26

Dear, This is Shubhrajyoti Panda, research scholar at Birla Institute of Technology, Hyderabad. I am using 6XG5 PDB ID for my work. But in this particular protein I want to show the distance between particular residues. But when I am going to show manually or through command it is showing the following error. Distance between PHE 31.A CA and GLY 15.A CA: 15.891 Distance between PHE 31.A CA and MET 16.A CA: 19.088 Distance between PHE 31.A CA and ALA 19.A CA: 15.571 Distance between PHE 31.A CA and ILE 14.A CA: 14.072 Error while sourcing chimera_distances.cmd, line 14: "distance :31.A@CA :45.A@CA" *Exactly two atoms/axes/planes must be selected. You selected 3.* But in the protein structure there is only one 45th number residue. But I could not understand why it is showing selected 3 repeatedly. Kindly help me. Thanks & Regards Shubhrajyoti Panda Phone: +91-7001855842 Email: panda.jyoti.shubhra(a)gmail.com

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Question about AlphaFold prediction in ChimeraX
by Ehsaneh Khodadadi 16 Mar '26

16 Mar '26

Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi

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how to increase the size of the metal spheres
by 吴林 12 Mar '26

12 Mar '26

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No command line on Apple silicon M1
by Marco Sette 12 Feb '26

12 Feb '26

Hi all, the command line is not working on apple silicon with the latest Chimera versions. Do you have suggestion how to solve the problem? Thanks for your help. Best regards Marco -- Marco Sette, PhD Associate Professor of Molecular Biology Department of Chemical Sciences and Technology The University of Rome, "Tor Vergata" Via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Conference Announcement: 38th Molecular Modelling Workshop in Erlangen, Germany - March 9/10 2026
by Harald Lanig 30 Jan '26

30 Jan '26

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md movie
by Natesh Singh 29 Jan '26

29 Jan '26

Dear support team, I am trying to make a md movie using the md movie utility of Chimera 1.19. But it seems that in the end, it is creating a kb size mp4 file with no movie inside. Can anyone help me in this regard? sincerely Natesh

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Re: md movie
by Tom Goddard 29 Jan '26

29 Jan '26

Hi Natesh, Glad you figured it out. Probably image save with 3x3 supersampling is not working because of a limitation of your graphics driver. Tom > On Jan 28, 2026, at 11:56 PM, Natesh Singh <singh.natesh(a)gmail.com> wrote: > > Hello Tom, > I just found that when I do supersample 2X2, it creates the movie, but not with supersample 3X3 or 4X4. I do not know the reason why it is not generating movies with higher supersamples. But I am glad that it worked out at 2X2, which is sufficient for my purposes. > Thanks for your feedback > sincerely > Natesh > > On Thu, Jan 29, 2026 at 7:54 AM Natesh Singh <singh.natesh(a)gmail.com <mailto:singh.natesh@gmail.com>> wrote: >> Hello Tom, >> Thanks for your reply. >> But I am trying to make a movie from a single PDB MD trajectory file using the MD Movie plugin in Chimera. >> In the past, I had successfully used this plugin to create movies from MD simulation trajectories, but suddenly it is not working. It is creating empty movies, so I am not able to understand what happened in the meantime. Could you reflect on this about the possible reasons, some software update needed, etc? It seems that at the end of playing frames ffmpeg.exe opens up, but it is not able to transform the frames into a video file. I see the empty screen of ffmpeg.exe, followed by an empty video file. >> Many thanks >> Natesh >> >> On Thu, Jan 29, 2026 at 2:25 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> Hi Natesh, >>> >>> The usual cause of empty movies is that you did not use the "wait" command in your movie recording. That is the command that waits for frames to be rendered. Here is an example set of command to make a movie rotating a structure 90 degrees. >>> >>> open 1a0m >>> movie record ; turn y 1 90 ; wait 90 ; movie encode ~/Desktop/test.mp4 >>> >>> Here is a Chimera movie making tutorial that gives more examples >>> >>> https://www.cgl.ucsf.edu/chimera/data/nih-oct2012/movies.html >>> >>> and here is detailed Chimera movie documentation >>> >>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html >>> >>> Tom >>> >>> >>>> On Jan 28, 2026, at 5:04 PM, Natesh Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>>> >>>> Dear support team, >>>> I am trying to make a md movie using the md movie utility of Chimera 1.19. But it seems that in the end, it is creating a kb size mp4 file with no movie inside. >>>> Can anyone help me in this regard? >>>> sincerely >>>> Natesh >>>> _______________________________________________ >>>> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> >>>> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> >>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ >>>

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Re: Chimera Scripting Query
by Eric Pettersen 20 Dec '25

20 Dec '25

Hi Ali, You might be able to make a non-GUI script using MatchMaker's match() function. However, the Match→Align functionality is completely intertwined with its GUI and there is no way to access it in a non-GUI fashion. ChimeraX does a much better job of separating functionality so that it is available both to scripting and the GUI, but Match→Align hasn't been implemented in ChimeraX (yet). --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 19, 2025, at 9:52 AM, Ali, Asif <maa32(a)illinois.edu> wrote: > > Hi Eric, > > I wanted to script running MatchMaker and MatchAlign on pdb structures in a directory and extract RMSD headers without having to use the GUI application? > > Thank you for your time. > > > Best Regards, > > Mr. Asif Ali (He/Him/His) > PhD Student, Bioinformatics: Crop Sciences > University of Illinois Urbana-Champaign > Researcher @ GCA Lab | NSRC > Teaching Assistant | HORT 105 > ✉ maa32(a)illinois.edu <mailto:maa32@illinois.edu> linkedin.com/in/asif1/ <http://linkedin.com/in/asif1/> > > <http://illinois.edu/> > Under the Illinois Freedom of Information Act any written communication to or from university employees regarding university business is a public record and may be subject to public disclosure.

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Fwd: [Chimera] Request for download link: UCSF Chimera for macOS High Sierra
by Elaine Meng 18 Dec '25

18 Dec '25

> Begin forwarded message: > > Subject: [Chimera] Request for download link: UCSF Chimera for macOS High Sierra > Date: December 16, 2025 at 10:10:53 PM PST > Cc: Oleg Murashko <o.murashko(a)gmail.com> > > Dear Chimera Team, > > I hope you are well. > > Could you please provide a download link for the last version of UCSF Chimera > that is compatible with macOS 10.13 (High Sierra)? > > We are currently maintaining a legacy macOS system for compatibility reasons, > and newer versions of Chimera / ChimeraX are not supported on this OS. > > Thank you very much for your time and assistance. > > Best regards, > Oleg >

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