- Chimera-users - RBVI Mailing Lists

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

30 Jan '26

1 0

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

3 3

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/ >>>

1 0

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.

2 3

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 >

3 3

DOWNLOAD ISSUE IN WEBSITE
by sOum 18 Dec '25

18 Dec '25

Dear Developers team it's been one day since i have been trying to download "Chimera" from your website but the download speed is very poor (Some bytes per Second) . This issue is being faced by all . It needs to be fixed As Soon As Possible ! Waiting for your Reply .

2 1

chimera display window issue
by Rechiche, Othman 10 Dec '25

10 Dec '25

Hi Chimera team, I’d like to bring to your attention an issue I’m encountering with the model display window (see attached images). As shown, the window appears incomplete. This problem started only after upgrading to the new macOS Tahoe—I did not experience it on macOS Sequoia. I’m currently using chimera-alpha-mac64.dmg (MD5: 555a52a5b12e1a617013213bf0f66c8d), the latest daily build. Could someone please take a look and advise on a possible solution? I would greatly appreciate your help. Thank you very much. Best regards, Othman ______________________________________ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.

2 3

Write_DMS was not found
by 肖磊 09 Dec '25

09 Dec '25

Greetings, I can not find WRITE_DMS in ChimeraX. Is WRITE_DMS removed?

2 1

CHIMERA X1.11 RELEASE - 12.01.25
by Laura Oliveira Gomes 01 Dec '25

01 Dec '25

Dear ChimeraX Support Team, I am writing to ask about the release of *ChimeraX version 1.11*, which is expected today. Is it already available for download? Since I need to use the software today, would you recommend waiting for the new release or downloading the previous version for now? Thank you, Laura Oliveira Gomes

2 2

About present the result of DiffDock using Chimera
by galxj 19 Nov '25

19 Nov '25

Dear Sir/Madam, I am a user of the Chimera software. I have obtained some molecular docking results from DiffDock, where the ligand molecules are in SDF format and the receptor protein is in PDB format. May I ask if it's possible to view the docking results using Chimera? I have tried many times but keep encountering errors. I also attempted to convert the SDF file to PDB format and opened both files together. Although both molecules are displayed, it is clear that the docking has not been performed correctly. Best Regards, Alei Geng

2 1