November 2024 - ChimeraX-users - RBVI Mailing Lists

VR on Apple silicon?
by David Bhella 22 Nov '24

22 Nov '24

Has anyone managed to make chimeraX VR work on an ARM Mac with meta quest 3? Possible or am I flogging a dead horse? D Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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protein void volume or enclosed space
by Vitali James 21 Nov '24

21 Nov '24

Dear Chimera support, Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x. best, James

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help browser and embedded pdf's
by John Monroe Heumann 21 Nov '24

21 Nov '24

Hi, Am I correct that ChimeraX help browser currently can not automatically open links to pdf's (requiring you to download the file instead)? If so, would this be a reasonable enhancement request or do the pdf reader licensing requirements make it impractical? Thanks! -jh-

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ChimeraX on a tablet ?
by GOVAERTS Cédric 20 Nov '24

20 Nov '24

Hi ChimeraX team I wanted to know if ChimeraX can run on a tablet, either Ipad (M2 or M4 chips) of a Windows tablet (either Intel or Qualcomm Snapdragon) ? Obviously not for using it as main workstation, but rather check structural features while on the move. Thanks Cedric - Prof. Cedric Govaerts, Ph.D. Biochemistry & Structural Biology Universite Libre de Bruxelles - Campus Plaine. Building BC, Room 1C4 203 - Phone :+32 2 650 53 77 Boulevard du Triomphe, Acces 2 1050 Brussels - Belgium

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Adding a Covalently Bound PLP to an AlphaFold Model
by Omar De Bei 20 Nov '24

20 Nov '24

Dear ChimeraX Community, I’m reaching out for advice on what is likely a simple issue, but I’m stuck and would greatly appreciate your input. I’m currently working on a PLP-dependent enzyme and have generated its structure using AlphaFold3. Unfortunately, AlphaFold3 does not include PLP as a preset ligand. To address this, I’m attempting to manually add the PLP to the predicted structure based on homology with other PLP-dependent enzymes. Here’s where I’m facing trouble: The PLP forms a covalent bond with a lysine residue in the active site. After aligning my AlphaFold-predicted structure with the PDB structure of a homologous enzyme, I managed to position the PLP within the predicted structure. However, the lysine residue is not in the correct orientation to form the covalent bond. I’ve tried changing the lysine’s rotamer to improve the position, but it’s still not quite right. I was considering performing a local minimization of the structure to refine the geometry, but I’m unsure how to do this in ChimeraX. Does ChimeraX offer a tool or feature for local minimization that could help in this scenario? If so, could you guide me on how to proceed? Thank you in advance for your help! Best regards, Omar

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Bundle Sample Code
by Lou Holland 19 Nov '24

19 Nov '24

Hello, I work with Jon Agirre at the University of York and am about to start work on developing a privateer bundle for ChimeraX for glycan validation. I have been working through some of the very helpful tutorials and was planning to work through this page as I started building the bundle: https://www.rbvi.ucsf.edu/chimerax/docs/devel/writing_bundles.html I tried to download the sample code ( https://www.cgl.ucsf.edu/chimerax/cgi-bin/bundle_sample.zip) linked in the "Bundle Sample Code" section so that I could use it as a starting point to edit for the privateer bundle, but it seems that the sample code is not currently available. Is this something that you can help with? Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

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Question about commercial license for ChimeraX
by Gleb NOVIKOV 18 Nov '24

18 Nov '24

Dear ChimeraX Development Team, I hope this message finds you well. I am writing as an enthusiastic user of your remarkable software, which has been instrumental in both my academic and educational pursuits. Recently, I was approached by a small company interested in commissioning visualizations as part of a collaborative effort. I would like to inquire whether you offer a specific commercial license suitable for such freelance engagements. Additionally, I would be delighted to contribute to your website by sharing some of my visualizations of molecular systems, should this be of interest to your team. Thank you very much for your time and consideration. I look forward to your response. Best regards, Gleb

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Question the lattest ChimeraX-1.9
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear ChimeraX users! I am testing the new ChimeraX 1.9 release, via creating a short movie demonstrating an X-ray structure with basic features (without molecular dynamics). I noticed that my computer (using an Apple Silicon chip) gets quite hot during the frame rendering process (prior to encoding). In the previous release (1.8), the resource usage didn't seem as intense. Have there been any changes or optimizations in the new version that could explain this increased resource demand? Thank you in advance! Enrico

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Fuzzy colour boundaries in protein cartoon
by James Lingford 18 Nov '24

18 Nov '24

Dear ChimeraX team and users, Is there a way to set colours of individual atoms to have a fuzzy boundary with the surrounding cartoon colour? Example picture attached. Normally, colouring individual atoms will create a solid line between one colour and the next. But is there a setting to change this? Many thanks

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Modelling of missed loop fragments in multi-chain structure
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico

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