- ChimeraX-users - RBVI Mailing Lists

Issue with lighting and silhouettes
by Alessio Nocentini 20 Jul '25

20 Jul '25

Hello, I need your support again for another issue I am meeting in using ChimeraX. Unlike Chimera, I cannot find the lighting panel, which was very useful to adjust lights. Moreover, when I have a protein surface, the silhouettes are not complete in ChimeraX (black square in figure). I attach the same figure done with the 2 softwares. In chimera X I cannot increase the lighting in the active site. Can you help? Thank you Best regards Alessio [image: Chimera.png] [image: ChimeraX.png] -- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

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help
by mariela Urrutia 17 Jul '25

17 Jul '25

I want to unsubscribe .Thanks you.Mariela On Monday, July 14, 2025 at 04:00:15 PM GMT-3, chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> wrote: Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. contacts (mariela Urrutia) 2. Re: contacts (Elaine Meng) 3. Re: Inquiry About Training for ChimeraX Plugin Development (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 14 Jul 2025 13:08:40 +0000 (UTC) From: mariela Urrutia <urrugada(a)yahoo.com> Subject: [chimerax-users] contacts To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <1518652022.1318836.1752498520245(a)mail.yahoo.com> Content-Type: multipart/alternative; boundary="----=_Part_1318835_1564174829.1752498520244" Hello, Could you tell me please how to get the contacts of a residue in a list and in the molecule representation?Thanks you in advance.Mariela

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ChimeraX Appreciation and Feature Suggestion (+ New #ChimeraX Tag on image.sc)
by José Jorge Ramírez Franco 16 Jul '25

16 Jul '25

Hi there, First of all, thank you for this outstanding piece of software. ChimeraX is truly invaluable and has become an essential tool in my workflow. As a microscopist working primarily with light microscopy (particularly confocal and light-sheet imaging) I’ve found ChimeraX’s rendering capabilities to be far superior to most tools currently available. I’ve even recommended its use several times on the image.sc forum <https://image.sc>, especially for rendering high-quality visualizations. In fact, I recently noticed that there was no #chimerax tag on the forum (surprisingly!) so I took the liberty of creating one. You can find the related post here: https://forum.image.sc/t/3d-multichannel-surface-rendering-from-z-stacks-na… While I have this opportunity, I’d like to *suggest a feature* that I believe would significantly enhance ChimeraX’s utility for large-scale light-sheet microscopy datasets: *support for .tiff files larger than 4 GB* . These large file sizes are quite common in light-sheet acquisitions, and the ability to open them natively in ChimeraX would be a substantial benefit to researchers in this field. Thank you once again for all the incredible work that goes into developing and maintaining ChimeraX. It’s deeply appreciated. Warm regards, J -- J. Jorge Ramírez-Franco PhD Institut de Neurosciences de la Timone, SpiCCI Team Faculté de Médecine 27, boulevard Jean Moulin 13005 Marseille, France

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Directed camera mouvement along cartoon chain
by Enrico Desperados 16 Jul '25

16 Jul '25

Dear ChimeraX users! I would like to create an artistic movie for an X-ray structure making an impression that I am running on the protein cartoon like on the serpentine road. I have tried the following trivial algorithm: view :1 clip false; zoom 0.6; wait 30 view :2 clip false; zoom 0.6; wait 30 view :3 clip false; zoom 0.6; wait 30 view :4 clip false; zoom 0.6; wait 30 ... view :200 clip false; zoom 0.6; wait 30 However, It just moved the camera focusing on each residue, without giving the impression of movement along the protein chain. Do we have a special orient option that could introduce such smooth movements ? Many thanks in advance! Enrico

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eachChain option for fitmap?
by Oliver Clarke 15 Jul '25

15 Jul '25

Hi, Fitmap has on option to fit each model sequentially (eachModel). Would it be possible in a future version to add an "eachChain" option to fit each polymer chain in a mult-chain model independently? This would be useful when quickly fitting oligomeric models to an EM map. Alternatively, is there another quick way to do this? I thought about using perframe, but that only take numerical ranges, not alphabetical Cheers Oli

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Inquiry About Training for ChimeraX Plugin Development
by Rafat Hasan Khan 14 Jul '25

14 Jul '25

Dear ChimeraX Team, I am part of a research group working with Dr. Amitava Roy (University of Montana). We plan to develop a plugin, but when we initially started using your documentation with version 1.9 (2024-12-11), we failed to make it work despite following the guides on "Bundle Example: Add a Qt-based Tool." Could you please let us know if there are any training programs, workshops, or additional resources available for developers? Any help or direction would be greatly appreciated. Thank you for your time. -- Best Rafat

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contacts
by mariela Urrutia 14 Jul '25

14 Jul '25

Hello, Could you tell me please how to get the contacts of a residue in a list and in the molecule representation?Thanks you in advance.Mariela

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Map resolution range values
by Rayees Mattoo 10 Jul '25

10 Jul '25

Hi, How to extract Map resolution range values from a resmap.mrc file for the Table 1 validation (for publication) using chimeraX? Other suggestions, using different methods to extract the map res range values are also welcome. Best

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How to get just model name
by Alexandra Zahradnikova 09 Jul '25

09 Jul '25

Dear All I would like to extract just the model name (as a variable) from a model, to write into an output file with other data. However I am not able to find in the help how to do it - I can output all model information ("Model info") to the log but not to see just model name. Is that possible? Thanks in advance Best regards Sasha

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XYZ basis vectors
by Jan Hofmann 09 Jul '25

09 Jul '25

Hello, how can I show the XYZ basis vectors somewhere next to my structure in ChimeraX? I found the .bild datei but I don't want the arrows in my structure, rather outside, next to it, like in Crystalmaker. It would be really helpful to have the basis vectors to compare orientations with other images. Thanks a lot. Best, *Jan Hofmann, M.Sc.* *PhD Candidate, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 577, Chemistry

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