November 2025 - ChimeraX-users - RBVI Mailing Lists

Problem opening local small-molecule CIF file
by Ute Roehrig 24 Nov '25

24 Nov '25

Hello, I'm having problems opening a locally stored small-molecule cif file. For example, the following runs without problems: open ccd:pim But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error: open PIM.cif -> No mmCIF models found. open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file? open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file? Thank you in advance for your help, Ute

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Re: Problem with modeller execution location
by Alexandra Zahradnikova 24 Nov '25

24 Nov '25

Dear Vinita, In the menu item Structure Prediction/Model Loops or Modeller Comparative there are boxes in which you insert the license key (password) – see the screenshots. Best regards Sasha From: Vinita Pant [mailto:vinipant78@gmail.com] Sent: Saturday, November 22, 2025 18:26 To: Alexandra Zahradnikova Subject: Re: [chimerax-users] Re: Problem with modeller execution location Thank you for your response. However, I did not find any option to input the MODELLER password. Since I am not very tech-savvy, could you please guide me? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Sat, 22 Nov 2025 at 21:22, Alexandra Zahradnikova <alexandra.zahradnikova(a)savba.sk> wrote: Dear Vinita, You have to input the MODELLER password into the ChimeraX interface before starting the program. You will get the password by e-mail when you register with the Modeller web-page. Best Sasha From: Vinita Pant via ChimeraX-users [mailto:chimerax-users@cgl.ucsf.edu] Sent: Saturday, November 22, 2025 15:43 To: ChimeraX Users Help Subject: [chimerax-users] Re: Problem with modeller execution location Dear Elaine, I also tried reinstalling Modeller. But the problem persists. I have attached the image showing the error. Is there a way to manually fix this in Chimera? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025 at 22:41, Vinita Pant <vinipant78(a)gmail.com> wrote: Thank you for the clarification. Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025, 10:39 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: The errror message is not about the path/location. It is about the license key, which you have to enter into the dialog directly. Please read the help: > https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key If you can't find the key in your local installation just follow the instructions/links in the above to get another key from the Modeller developers. Elaine > On Nov 18, 2025, at 8:59 AM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you for the information. Yes I have been using the academic version of Modeller directly. I tried locating the modeller path inside chimera. It still didn't work. > > Thanks and Regards > Vinita Pant > Doctoral Student (SRF) > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > Mobile No.: +91 9536940943 > > On Tue, 18 Nov 2025, 10:26 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: > Hi Vinita, > This error message is not about the location. As it says in the message, you have to get a license key for Modeller, which is obtained from the Modeller developers. > > This is all explained in the documentation, e.g. shown by clicking the Help button on the Model Loops dialog. See requirement #3 in the documentation: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key> > > You would need to enter that license key into the tool as described. When you say "successfully using Modeller for homology modeling" I don't know if you meant from inside ChimeraX, or just using Modeller directly. If you were doing it from inside ChimeraX, you should have already gotten this license key and entered it into the ChimeraX dialog. If you were doing it directly with Modeller installed on your own computer, I don't know where the license key is kept. Probably somewhere in the Modeller installation. > > 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 Nov 17, 2025, at 11:04 PM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Dear ChimeraX Team, > > I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. > > I would appreciate your guidance in resolving this matter. > > > > Thanks and Regards > > Vinita Pant > > Doctoral Student (SRF) > > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > > Mobile No.: +91 9536940943 > > _______________________________________________ > 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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Problem with modeller execution location
by Vinita Pant 22 Nov '25

22 Nov '25

Dear ChimeraX Team, I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. I would appreciate your guidance in resolving this matter. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

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Chimera X with Apple Vision Pro
by Wolf, Inga 21 Nov '25

21 Nov '25

Dear Chimera X and Chimera developers, I'm a staff member of the Max-Planck-Institute of Biochemistry near Munich, Germany. At the moment we use Vive Pro virtual glasses to create a 3D picture of our biological structures that have extensions to be showed in Chimera X (.wrl, .mrc ...). Chimera X and the glasses can be connected. Vive Pro is now 8 years old and we think of buying Apple Vision Pro glasses. Can you please tell me if Chimera X or Chimera can talk to these glasses? Is there a possibility to see the structures in these glasses? Thank you in advance for your answer. Best regards, Inga Wolf Inga Wolf Cell and Virus Structure John Briggs [1685544407897] MAX PLANCK INSTITUTE OF BIOCHEMISTRY Am Klopferspitz 18 | 82152 Martinsried | Germany Phone: +49 (89) 8578 - 2634 iwolf(a)biochem.mpg.de<mailto:name@biochem.mpg.de> http://www.biochem.mpg.de/briggs<http://www.biochem.mpg.de/>

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Predicting and modeling post-translationally modified C-terminal endings
by Parks, Ryssa 21 Nov '25

21 Nov '25

Hello, I am trying to predict and model a peptide docking to a receptor protein using ChimeraX's AlphaFold interface, and I was wondering if there is any way to specify post-translational modifications in the AlphaFold input function in ChimeraX? Our peptide has an amidated C-terminus, and my searches online have not yielded much success. Thank you, Ryssa Parks

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Navigating to a OneDrive folder prompts a wholesale download
by David Bhella 20 Nov '25

20 Nov '25

Dear ChimeraX users and team, I am wondering if anyone can advise how to stop OneDrive trying to download the contents of every folder I navigate through when trying to e.g. save an image or open a file? I haven’t seen this behaviour with any other software, but as I maintain a lot of my work on OneDrive, it would be nice to be able to interact directly with the working folder. At the moment I need to work on a local folder and then copy files across when saving, and open files through finder rather than the ChimeraX dialog, otherwise my Mac locks up while it tries to download everything in every folder it sees. Thanks, D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [cid:image002.png@01DAE420.99202CC0] [Logo, company name Description automatically generated]

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AI spam
by Eric Pettersen 18 Nov '25

18 Nov '25

Hi all, We have made some further adjustments to try to prevent these AI spams posts you have seen over the last few days. We are hopeful, but you never can be sure... --Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX languages
by Nicolas Caudron - IA-IPR SVT 18 Nov '25

18 Nov '25

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Emirates Estate
by soradae＠mailbox.in.ua 18 Nov '25

18 Nov '25

Real Estate in UAE https://emirates.estate/

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Listing cavity contacting residues
by George Tzotzos 17 Nov '25

17 Nov '25

Hi everyone, I’ve used kvfinder and the command: coulombic (#1 & protein) surfaces #1.1.1 offset -1 select #!1 & (#!1.1.1 @< 3.5)185 atoms, 163 bonds, 34 residues, 1 model selected Is there a way to list the 34 residues? Have a good day George

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