February 2023 - ChimeraX-users - RBVI Mailing Lists

Update pdb model in cxs session
by 张一小 28 Feb '23

28 Feb '23

Hi, I'm using ChimeraX to prepare figures. I saved a session containing several pdb files and maps. (The pdb files were saved in the CXS file right?) Now, I manually adjusted one of the models in Coot. Is there a way to update the old model with the new one in the session so that all the settings, such as colors, views, showing residues, hidden ribbons can be kept and applied?" Thanks, Yixiao

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Rotating/moving a chain to a different site
by Lohry, David 27 Feb '23

27 Feb '23

Hello! I am working with a protein dimer with DNA from a crystal structure. The dimer is composed of 2 chains (chain A and chain B) I would like to be able to place one of the chains on a different region of DNA and at a slightly different position. The only tool that I could find was the Movement Mouse Mode in Chimera original. Is there a way to do this a bit more mathematically (keeping the chain in tact)? Move 50 angstroms in the x direction, rotate chain by 30 degrees, etc . Also, I need it to update the actual coordinates in the PDB when saved so it can't be something that just affects the visual output. Thank you!

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Question!
by Matthew Wengler (TSL) 26 Feb '23

26 Feb '23

Hello, I am a PhD student studying the downstream signalling events of a kinase in a fungal plant pathogen. We have differential phosphopeptide data of the kinase itself over a time course during plant infection (i.e., four residues on this kinase are differentially phosphorylated during stages of infection). I had a vision of showing a movie that incorporated the phosphorylated residues x phosphorylation abundance x time on the kinase’s tertiary structure and was wondering if this could be possible with Chimera X: * The tertiary structure would be displayed in grey * The phosphorylated residues would be highlighted in blue * A movie would be played and the highlighted residues would change colour based on phosphopeptide abundance over a time course (ranging from 0-100% abundance = blue -> red) I was wondering if this was currently possible. Alternatively (and maybe this is really the easiest way), because we only have ~6 time points, I could have 6 different stills of the protein with the residues highlighted corresponding to the phosphopeptide abundance values (blue-red 0-100%) and then piece them together in a 6 frame video that will loop…? I think I would prefer the colours to blend slower together dynamically than 6 harsh frames. Would there be a way to do this in Chimera? Thank you, Matt Wengler

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some question about the use of chimera x 1.4
by 游宠昭 24 Feb '23

24 Feb '23

Dear developers, Sorry to bother you. Recently, I notice that chimera x display the DNA/RNA in a different way from that in chimera, and I find that there is a option in chimera called ribbon spline containing two options:B-spline and cardinal which explain why DNA/RNA is displayed in different ways in two softwares. However, I can not find the related actions in chimera x: "ribbon spline" in chimera refers to what in chimera x and how can I adjust this parameter. Sincerely, Chongzhao You

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Help Generating a Volume to use for 2D classification template generation
by Joshua Denson 22 Feb '23

22 Feb '23

Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University

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Matchmaker on a subset of residues
by McClean, Phillip 22 Feb '23

22 Feb '23

Is it possible to use the Chimerax Matchmaker command to obtain the RMSD value between a subset or residues between two different proteins. Phil McClean

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Custom Toolbar Button
by Dominik Sordyl 22 Feb '23

22 Feb '23

Hi, Is there a possibility to add a button to the "File" section on the toolbar? I have installed custom plugin and it can be run from Tools --> General section, but I am wondering if there is a way to add a shortcut button to the toolbar. Best, Dominik

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Making a movie from a group in PDB file
by Aleksandar Donev 21 Feb '23

21 Feb '23

Hi, I am trying to create a simple animation of a demo molecular dynamics program https://github.com/stochasticHydroTools/DemoMD using either chimerax or chimera. The code creates a .pdb file that has multiple time frames in it, which show up in chimerax as a "group". How do I make chimera show the frames one by one and then make a movie out of that or save each frame as an image? I used to be able to do that in chimera but either the interface has changed or I have forgotten. I found lots of instructions about how to make movies by manipulating one data set (say rotating a molecule) but could not find anything about animation in time. Thanks, Aleks -- Aleksandar Donev, Professor of Mathematics Courant Institute of Mathematical Sciences Office: 1016 Warren Weaver Hall, New York University E-mail: donev(a)courant.nyu.edu Phone: (212) 992-7315; Fax: (212) 995-4121 Mailing address: 251 Mercer St, New York, NY 10012 Web: http://cims.nyu.edu/~donev

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Distance maps and all atom distances
by André Graça 17 Feb '23

17 Feb '23

Hi everyone! Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps? I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models? Cheers, André

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Image saving/exporting options
by Matthew Graneri 16 Feb '23

16 Feb '23

Hi there, I was wondering if there was an option to set the resolution of an image you want to export? In the older Chimera application, there were many more options open to you when you wanted to save an image (I’ve attached a screenshot of the old and new image saving screens for comparison). If not, is there any chance of implementing a resolution specification option sometime in the future? I was also wondering if it was possible to save images from ChimeraX as PDF files? I find that they usually maintain a high resolution without being particularly big, in terms of memory. Apart from that, really enjoying ChimeraX! Regards, Matthew

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