February 2023 - ChimeraX-users - RBVI Mailing Lists

Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 16 Nov '23

16 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

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Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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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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ChimeraX-users February 2023