January 2025 - ChimeraX-users - RBVI Mailing Lists

UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

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Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

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No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

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Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

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Question about the tool Find Cavities
by svle＠tiscali.it 16 Jan '25

16 Jan '25

Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio

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pb with alphafold error plot when we used dimer
by Jean-François Bureau 15 Jan '25

15 Jan '25

Hi, When I stimulate dimer using alphafold3, it is not possible to load the error plot since Chimerax is waiting to have the data of the first protein and find that of both. Best JF Bureau

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Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
by Elaine Meng 13 Jan '25

13 Jan '25

Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, 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 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2(a)gmail.com> wrote: > > Oh shoot! > You are right, > > I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html > I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced. > > Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow. > > This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf > > THANK YOU for answering on a Sunday!! > Anne-Frances > >

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abbreviation for transparentbackground please
by Anne-Frances Miller 12 Jan '25

12 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Problem upgrading to the latest version 1.9
by svle＠tiscali.it 09 Jan '25

09 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

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Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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